Mitochondrial DNA structure in the Arabian Peninsula

<p>Abstract</p> <p>Background</p> <p>Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.</p> <p>Results</p> <p>To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source.</p> <p>Conclusion</p> <p>Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.</p

A patient with typical clinical features of mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) but without an obvious genetic cause: a case report

<p>Abstract</p> <p>Introduction</p> <p>There are currently 23 missense point mutations and one 4 basepair deletion spanning different mitochondrial genes associated with mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The spectrum of mitochondrial DNA mutations in Arab patients with MELAS is largely unknown.</p> <p>Case presentation</p> <p>A standard clinical examination was carried out on a 34-year-old Saudi woman showing clinical features of MELAS. Fresh frozen muscle tissue was subjected to enzyme histochemical analysis. DNA was extracted from her leukocytes and muscle tissue, and the full mitochondrial genome was screened for base substitution mutations and deletions. Additionally, we screened the polymerase gamma-1 nuclear gene for mutations. The patient was negative for the most common m.3243 A>G MELAS mutation. Sequencing the full mitochondrial genome did not reveal any known or potentially pathogenic sequence changes. The polymerase gamma-1 gene was also free from mutations.</p> <p>Conclusion</p> <p>The clinical picture described here typically fits that observed in patients with MELAS or mitochondrial stroke-like events, but mutations in recognized genes (mitochondrial DNA and polymerase gamma-1 gene) were absent. We report the case of a patient with typical clinical features of MELAS, but without an obvious genetic cause.</p

Absence of mtDNA mutations in leukocytes of CADASIL patients

<p>Abstract</p> <p>Background</p> <p>Ultrastructural and biochemical abnormalities of mitochondria have been reported in skeletal muscle biopsies of CADASIL patients with mutations in the <it>NOTCH3 </it>nuclear gene. Additionally, it was proposed that <it>NOTCH3 </it>gene mutations may predispose the mitochondrial DNA (mtDNA) to mutations.</p> <p>Methods</p> <p>We sequenced the entire mitochondrial genome in five Arab patients affected by CADASIL.</p> <p>Results</p> <p>The mean number of mtDNA sequence variants (synonymous and nonsynonymous) in CADASIL patients was not statistically significantly different from that in controls (<it>p </it>= 0.378). After excluding haplogroup specific single nucleotide polymorphisms (SNPs) and proved silent polymorphisms, no known or novel pathologic mtDNA mutation(s) could be detected in any patient. Additionally, there was no difference in the prevalence of different mitochondrial haplogroups between patients and controls.</p> <p>Conclusion</p> <p>Our study group is too small for any valid conclusion to be made. However, if our observation is confirmed in larger study group, then mtDNA mutations or mitochondrial haplogroups may not be important in the pathogenesis of CADASIL.</p

Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Background: From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia.  Results: The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.  Conclusions: The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa

Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler(®) PCR amplification kit

Highlights: * GlobalFiler® PCR amplification kit was used to generate a reference dataset for the population of Saudi Arabia. * SE33, D12S391, and D1S1656 in this kit are more informative for the population of Saudi Arabia than any locus in the AmpFlSTR® Identifiler® PCR amplification kit

The growth hormone receptor gene deleted for exon three (GHRd3) polymorphism is associated with birth and placental weight.

Human growth hormone receptor (GHR) transcripts have two isoforms, full-length (GHRfl) or exon 3 deleted (GHRd3). An association of these isoforms has been found with small for gestational age (SGA) infants but does not influence adult height. The role of this polymorphism in the birth size spectrum in the general population is unclear

Eurasian and African mitochondrial DNA influences in the Saudi Arabian population

BACKGROUND: Genetic studies of the Arabian Peninsula are scarce even though the region was the center of ancient trade routes and empires and may have been the southern corridor for the earliest human migration from Africa to Asia. A total of 120 mtDNA Saudi Arab lineages were analyzed for HVSI/II sequences and for haplogroup confirmatory coding diagnostic positions. A phylogeny of the most abundant haplogroup (preHV)1 (R0a) was constructed based on 13 whole mtDNA genomes. RESULTS: The Saudi Arabian group showed greatest similarity to other Arabian Peninsula populations (Bedouin from the Negev desert and Yemeni) and to Levantine populations. Nearly all the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. Saudi Arabs had only a minority sub-Saharan Africa component (7%), similar to the specific North-African contribution (5%). In addition, a small Indian influence (3%) was also detected. CONCLUSION: The majority of the Saudi-Arab mitochondrial DNA lineages (85%) have a western Asia provenance. Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic expansion in Saudi Arabia