Dataset Information

Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

ABSTRACT: The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies.

SUBMITTER: Barral-Arca R

PROVIDER: S-EPMC4956223 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

Barral-Arca Ruth R Pischedda Sara S Gómez-Carballa Alberto A Pastoriza Ana A Mosquera-Miguel Ana A López-Soto Manuel M Martinón-Torres Federico F Álvarez-Iglesias Vanesa V Salas Antonio A

PloS one 20160721 7

The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on pa ...[more]

PMID: 27441366

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Project description:BackgroundTwo 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.ResultsTo 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.ConclusionAlthough 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.

Project description:BackgroundInbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations.A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history.ResultsThe domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ? including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ?, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds.ConclusionsHigh-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.

Dataset Information

Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

Publications

Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

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