The genetic landscape of Mediterranean North African populations through complete mtDNA sequences

Identifying signatures of positive selection in human populations from North Africa

Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries—the time of the Atlantic slave trade—thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the “greening” of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.

Genetic Diversity Analysis of the Chinese Daur Ethnic Group in Heilongjiang Province by Complete Mitochondrial Genome Sequencing

Mitochondrial DNA (mtDNA) has the characteristics of maternal inheritance, high mutation rate, high copy number, and no recombination. As the most powerful tool for studying the origin and evolution of modern humans, mtDNA has great significance in the research of population genetics and evolutionary genetics. Here, we provide new insights into the maternal genetic history of the Daur ethnic group by generating complete mitochondrial genomes from a total of 146 Daur individuals in China. We also collected the published complete mitochondrial genome sequences of 5,094 individuals from 56 worldwide populations as reference data to further explore the matrilineal genetic landscape of the Daur ethnic group. First, the haplotype diversity was 0.9943 ± 0.0019 and nucleotide diversity was 0.0428 ± 0.0210. The neutrality tests of the Daur group showed significant negative values and the mismatch distribution curve was obviously distributed in a unimodal pattern. The results showed that the Daur ethnic group has high genetic diversity and may have experienced recent population expansion. In addition, the main haplogroups of the Daur population were haplogroup D (31.51%), M* (20.55%), C (10.28%), F (7.53%), and B (6.85%), all of which were prevalent in northern China. It probably implies the northern Chinese origin of the Daur population. The PCA, F_ST, and phylogenetic analysis results indicated that the Daur group formed a cluster with East Asian populations, and had few genetic differences with the populations in northern China. More importantly, we found that disease-related mutation sites of the mitochondrial genome may be related to ethnic groups, which may have important implications for the prevention and occurrence of specific diseases. Overall, this study revealed the complexity and diversity of the matrilineal genetic background of the Daur ethnic group. Meanwhile, it provided meaningful data for the research on the diversity of the human genome.

Clinical and genetic spectrums of 413 North African families with inherited retinal dystrophies and optic neuropathies

Background

Inherited retinal dystrophies (IRD) and optic neuropathies (ION) are the two major causes world-wide of early visual impairment, frequently leading to legal blindness. These two groups of pathologies are highly heterogeneous and require combined clinical and molecular diagnoses to be securely identified. Exact epidemiological studies are lacking in North Africa, and genetic studies of IRD and ION individuals are often limited to case reports or to some families that migrated to the rest of the world. In order to improve the knowledge of their clinical and genetic spectrums in North Africa, we reviewed published data, to illustrate the most prevalent pathologies, genes and mutations encountered in this geographical region, extending from Morocco to Egypt, comprising 200 million inhabitants.

Main body

We compiled data from 413 families with IRD or ION together with their available molecular diagnosis. The proportion of IRD represents 82.8% of index cases, while ION accounted for 17.8%. Non-syndromic IRD were more frequent than syndromic ones, with photoreceptor alterations being the main cause of non-syndromic IRD, represented by retinitis pigmentosa, Leber congenital amaurosis, and cone-rod dystrophies, while ciliopathies constitute the major part of syndromic-IRD, in which the Usher and Bardet Biedl syndromes occupy 41.2% and 31.1%, respectively. We identified 71 ION families, 84.5% with a syndromic presentation, while surprisingly, non-syndromic ION are scarcely reported, with only 11 families with autosomal recessive optic atrophies related to OPA7 and OPA10 variants, or with the mitochondrial related Leber ION. Overall, consanguinity is a major cause of these diseases within North African countries, as 76.1% of IRD and 78.8% of ION investigated families were consanguineous, explaining the high rate of autosomal recessive inheritance pattern compared to the dominant one. In addition, we identified many founder mutations in small endogamous communities.

Short conclusion

As both IRD and ION diseases constitute a real public health burden, their under-diagnosis in North Africa due to the absence of physicians trained to the identification of inherited ophthalmologic presentations, together with the scarcity of tools for the molecular diagnosis represent major political, economic and health challenges for the future, to first establish accurate clinical diagnoses and then treat patients with the emergent therapies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02340-7.

Human Genomic Diversity Where the Mediterranean Joins the Atlantic

Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.

Genetic diversity of 15 autosomal STRs in a sample of Berbers from Aurès region in the Northeast of Algeria and genetic relationships with other neighbouring samples

Background: The history of the Aurès mountains and neighbouring areas, a large region of the East of Algeria, was part of the history of the ancient independent Berber kingdoms supposed to be the ancestors of the current Berber people. The genetic background of this region has not yet been clarified.Aim: The aims of our study were to investigate the genetic characteristics of 15 autosomal short tandem repeats (STRs) in a sample from these regions, to determine the degree of heterogeneity among Algerian and North African samples and to analyse the genetic relationships with other populations.Subjects and methods: Allele frequencies, forensic parameters and Hardy-Weinberg equilibrium (HWE) of 15 autosomal STRs included in the PowerPlex^® ESI 16 System were obtained from 308 individuals. Allele frequencies were used to determine the relationships with other populations.Results: All loci were highly polymorphic and no significant deviation from HWE was detected. Allele frequencies showed that the samples of Aurès region share genetic affinities with other Algerian, North African and Middle Eastern samples, with the exception of samples from Iran and Matmata.Conclusions: These markers revealed a genetic homogeneity between the Algerian and North African samples. The genetic affinities indicate that this sample could share a common ancestor with the Middle Eastern samples.

miRNA expression in advanced Algerian breast cancer tissues

Breast cancer is one of the commonest cancers among Algerian females. Compared to Western populations, the median age of diagnosis of breast cancer is much lower in Algeria. The objective of this study is to explore the expression of several miRNAs reported to be deregulated in breast cancer. The miRNAs miR-21, miR-125b, miR-100, miR-425-5p, miR-200c, miR-183 and miR-182 were studied on tumor and normal adjacent Algerian breast tissues using quantitative reverse transcription real time PCR, and the results were analyzed according to clinical characteristics. Compared to the normal adjacent tissues, miR-21, miR-183, miR-182, miR-425-5p and miR-200c were found to be upregulated while miR-100 and miR-125b were insignificantly deregulated. A positive correlation was noted among miR-183, miR-182 and miR-200c and among miR-425-5p, miR-183, miR-200c and miR-21. Further global miRNA microarray profiling studies can aid in finding ethnic specific miRNA biomarkers in the Algerian breast cancer population.

Multidisciplinary investigation of two Egyptian child mummies curated at the University of Tartu Art Museum, Estonia (Late/Graeco-Roman Periods)

Two ancient Egyptian child mummies at the University of Tartu Art Museum (Estonia) were, according to museum records, brought to Estonia by the young Baltic-German scholar Otto Friedrich von Richter, who had travelled in Egypt during the early 19th century. Although some studies of the mummies were conducted, a thorough investigation has never been made. Thus, an interdisciplinary team of experts studied the remains using the most recent analytical methods in order to provide an exhaustive analysis of the remains. The bodies were submitted for osteological and archaeothanatological study, radiological investigation, AMS radiocarbon dating, chemical and textile analyses, 3D modelling, entomological as well as aDNA investigation. Here we synthesize the results of one of the most extensive multidisciplinary analyses of ancient Egyptian child mummies, adding significantly to our knowledge of such examples of ancient funerary practices.

Human Leukocyte Antigens (HLA) Genes Association in Type 1 Diabetic Nephropathy

BACKGROUND

Diabetic nephropathy is a common worldwide multifactorial disease where involvement of genetic factors is well etablished. The aim of this study was to investigate the HLA genes implication in the development of type 1 diabetic nephropathy.

METHODS

We performed a case- control study where one hundred and fifty subjects were examined. Patients were divided in two groups; with and without type 1 diabetic nephropathy. HLA typing was performed using Polymerase Chain Reaction- Sequence Specific Oligonucleotide (PCR- SSO) method. HLA association to clinical phenotype and HLA haplotype analysis was also investigated.

RESULTS

HLA B*51 is increased in patients without type 1 diabetic nephropathy (7.14% vs. 0 %, P <0.05, OR= 0), however no other studied alleles seem to have any effect (all P>0.05). Haplotype analysis also does not reveal any significant association, however, A*02-B*18-DRB1*03-DQA1*05- DQB1*03 haplotype shows a tendency to be associated with the development of diabetic nephropathy (P = 0.05).

CONCLUSION

These results suggest a protective effect of HLA B*51 allele from type 1 diabetic nephropathy. However, further studies are required in order to clarify its potential implication as a protective marker.

Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza

Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.

Human variation in the shape of the birth canal is significant and geographically structured

The human birth canal shows a tight fit with the size of the neonate, which can lead to obstetric complications. This is not the case in other apes, and has been explained as the outcome of conflicting evolutionary pressures for bipedal locomotion and parturition of a highly encephalized fetus. Despite the suggested evolutionary constraints on the female pelvis, we show that women are, in fact, extremely variable in the shape of the bony birth canal, with human populations having differently shaped pelvic canals. Neutral evolution through genetic drift and differential migration are largely responsible for the observed pattern of morphological diversity, which correlates well with neutral genetic diversity. Climatic adaptation might have played a role, albeit a minor one, with populations from colder regions showing a more transversally oval shape of the canal inlet. The significant extent of canal shape variation among women from different regions of the world has important implications for modern obstetric practice in multi-ethnic societies, as modern medical understanding has been largely developed on studies of European women.

African genetic diversity provides novel insights into evolutionary history and local adaptations

Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.