Gender and population history: Sex bias revealed by studying genetic admixture of Ngazidja population (Comoro Archipelago)

Allelic and haplotypic data of MHC class II Alu insertions in Ngazidja (Comoros archipelago) and insight on its historical biology

This study aimed to analyse, for the first time, five MHC class II polymorphic Alu insertions in a population with a strong Sub-Saharan African genetic background: the Ngazidja islanders and compare its allelic and haplotypic data with Worldwide populations. The genotyping was performed in 80 individuals, using simple PCR and agarose gel electrophoresis methods. Allele and haplotype frequencies, genetic diversity, Hardy-Weinberg equilibrium deviations, normalized deviate of homozygotes and pairwise linkage disequilibrium were estimated. The phylogenetic analyses included the available population data. In Ngazidja, the MHC class II Alu insertion frequencies ranged from 0.119 for AluORF10 to 0.588 for AluDPB2. Concerning haplotypes, the most predominant were the ones with only the AluDPB2 insertion allele (AluDPB2*2-AluDQA2*1-AluDQA1*1-AluDRB1*1-AluORF10*1), followed by the theoretical ancestral haplotype with no Alu insertions (AluDPB2*1-AluDQA2*1-AluDQA1*1-AluDRB1*1-AluORF10*1) and finally the haplotype with the AluDPB2 and AluDQA1 Alu insertions (AluDPB2*2-AluDQA2*1-AluDQA1*2-AluDRB1*1-AluORF10*1) with frequencies of 19.2%, 15% and 12.9%, respectively. In the phylogenetic analyses, our results indicate that the Ngazidja people are genetically differentiated from the other populations of the analysis; we found also a new haplotype that can be probably characteristic of Sub-Saharans and finally confirm the usefulness of these markers as genetic and evolutionary tools for studying genetic variations among populations of different origins.

Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia

The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.

Admixture Indicative Interval (AII): a new approach to assess trends in genetic admixture

The genetic admixture is a dynamic and diachronic process, taking place during a great number of generations. Consequently, a sole admixture rate does not represent such an event and several estimates could help to take into account its dynamics. We developed an Admixture Indicative Interval (AII) which gives a mathematical key to avoid this problem by integrating several admixture estimators and their respective accuracy into a single metric and provides a trend in genetic admixture. To illustrate AIIs interests in admixture studies, AII were calculated using seven estimators on two sets of simulated SNPs data generated under two different admixture scenarios and were then calculated from several published admixed population data: a Comorian population and several Puerto-Rican and Colombian populations for recent admixture events as well as European populations representing the Neolithic/Paleolithic admixture for an older event. Our method provides intervals taking properly the variability and accuracy of admixture estimates into account. The AII lays in the intuitive interval in all actual and simulated datasets and is not biased by divergent points by the mean of a double-weighting step. The great quantity of heterogeneous parental contributions is synthesized by a few AII, which turn out to be more manageable and meaningful than aplenty variable point estimates. This offers an improvement in admixture study, allowing a better understanding of migratory flows. Furthermore, it offers a better assessment of admixture than the arithmetic mean, and enhances comparisons between regions, samples, and between studies on same population.

Multiple ethnic origins of mitochondrial DNA lineages for the population of Mauritius

This article reports on the first genetic assessment of the contemporary Mauritian population. Small island nodes such as Mauritius played a critical role in historic globalization processes and revealing high-resolution details of labour sourcing is crucial in order to better understand early-modern diaspora events. Mauritius is a particularly interesting case given detailed historic accounts attesting to European (Dutch, French and British), African and Asian points of origin. Ninety-seven samples were analysed for mitochondrial DNA to begin unravelling the complex dynamics of the island's modern population. In corroboration with general demographic information, the majority of maternal lineages were derived from South Asia (58.76%), with Malagasy (16.60%), East/Southeast Asian (11.34%) and Sub-Saharan African (10.21%) also making significant contributions. This study pinpoints specific regional origins for the South Asian genetic contribution, showing a greater influence on the contemporary population from northern and southeast India. Moreover, the analysis of lineages related to the slave trade demonstrated that Madagascar and East Asia were the main centres of origin, with less influence from West Africa.

Madagascar: A History of Arrivals, What Happened, and Will Happen Next

Most of the ancestors of today's human and animal populations reached Madagascar over the last 65 million years, by a variety of routes at a variety of times. Settlers encountered a big, isolated island with an unpredictable climate and a wide array of landscapes. Although patterns of diversification were driven by different mechanisms in humans and animals, the complex interplay between historical contingency and responsiveness to local conditions is evident in both.

Global climate change will affect Madagascar, although exactly how remains unclear, and the immediate impact of human activity on the island is overtaking that of gradual global change. Three themes in this review bear on the future: the continuing impact of recent, cataclysmic events on modern communities of people, plants, and animals; Madagascar's long and dynamic environmental history; and the complicated history of how people settled and interacted with the island's landscapes. A deeper understanding of all three can contribute to wise decision making in the coming years.