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Post by Admin on Apr 2, 2024 13:50:03 GMT
Genomic landscape of human diversity across Madagascar SIGNIFICANCE The origins of the Malagasy raise questions about ancient connections between continents; moreover, because ancestors are fundamental to Malagasy society, Malagasy origins is also a heated topic around the country, with numerous proposed hypotheses. This study provides a comprehensive view of genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) based on a sampling of 257 villages across Madagascar. The observed spatial patterns lead to a scenario of a recent and sex-biased admixture between Bantu and Austronesian ancestors across the island. Moreover, we find geographical influences creating subtle signals of genetic structure that are independent of the Bantu/Austronesian admixture, suggesting that recent history has a role in the genomic diversity of the Malagasy. Keywords: Indian Ocean, proto-globalization, genetics, Malagasy origins, genome-wide data www.ncbi.nlm.nih.gov/pmc/articles/PMC5559028/ |
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Post by Admin on Apr 2, 2024 21:19:55 GMT
 Our results indicate that across the entire country all Malagasy individuals share recent Austronesian and Bantu ancestry (Fig. 6). We identified a recent split of the proto-Malagasy population from southern African Bantus around 1,500 y BP and an older split from south Borneo between 3,000 and 2,000 y BP. This result suggests that Indonesians populations may have arrived on Madagascar before African populations. |
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Post by Admin on Apr 3, 2024 21:22:47 GMT
Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.
Ancient long-distance voyaging between continents stimulates the imagination, raises questions about the circumstances surrounding such voyages, and reminds us that globalization is not a recent phenomenon. Moreover, populations which thereby come into contact can exchange genes, goods, ideas and technologies (1). One of the most remarkable examples of such ancient intercontinental contact is the Malagasy, the Austronesian-speaking population that occupies Madagascar. Numerous theories have been proposed to explain the origin of the human diversity observed in Madagascar (summarized in ref. 2). Although historical, linguistic, ethnographic, archeological, and genetic studies confirm the dual African and Asian influences (3–11), no consensus exists regarding how, where, and when the two worlds met and merged. The lack of written history and the limited archeological evidence make it difficult to differentiate (i) founding myths and oral history, (ii) scientific hypothesis (iii), and pure speculation sometimes spread with political agenda. Because the ancestor “cult” is a fundamental aspect of Malagasy society, the roots of Malagasy population are a heated topic around the country. For instance, whether the Malagasy are of mainly African or Asian ancestry is still vigorously debated. Along with African and Austronesian connections (11), contributions from Arabic, Indian, Papuan, and/or Jewish populations have been suggested for a long time (12), as have the existence and heritage of the legendary first settlers of Madagascar, namely hunter-gatherers called variously “Vazimba,” “Kimosy,” or “Gola” (13).
Genetic data can illuminate population histories but are still limited and puzzling regarding Madagascar. Early studies in 1995 detected heterogeneity in Austronesian and Bantu ancestry according to the DNA loci studied (14, 15). In 2005, a study of mtDNA and Y chromosome variation in 37 Malagasy individuals identified approximately equal African and Indonesian contributions to both paternal and maternal Malagasy lineages (16). However, a later study of southeast Madagascar observed a strong sex bias, with the Austronesian ancestry appearing more conserved in the female gene pool, and a strong regional heterogeneity (17). Additionally, the first whole sequencing of mtDNA revealed that one maternal lineage thought to be of Austronesian origin (the M lineage) was actually a haplogroup (M23) specific to Madagascar, raising the possibility of a maternal heritage from hypothesized pre-Austronesian and pre-Bantu populations such as the Vazimba (13). However, the first study of genome-wide SNP data from southern Madagascar did not find any evidence of Vazimba heritage and instead proposed a recent (during the last millennium) admixture between Bantu-speaking and Austronesian-speaking groups (18). This study also argued for the predominance of African ancestry, in contradiction to a model-based study that suggested a maternal ancestry coming mainly from Asia (19).
These conflicting results suggest that the ancestry across Malagasy genomes may be highly heterogeneous according to the genetic loci and the geographical locations studied. Accordingly, a global study of maternal, paternal, and autosomal genetic variation across all of Madagascar is necessary to understand the settlement process fully. At present, the genetic ancestry of most of Madagascar remains unknown, and, given that the island is almost three times the size of Great Britain, settlement processes and admixture timing might have varied across the island. Thus, more comprehensive studies are needed to investigate the possibility of contributions of putative autochthonous populations and/or the existence of multiple waves of migration to Madagascar.
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Post by Admin on Apr 4, 2024 20:49:58 GMT
RESULTS Sampling Across 257 Villages. To address these issues, we present here a comprehensive study of Madagascar’s population based on a grid-based sampling encompassing 257 villages across the island (Fig. 1A). We collected data on genetic diversity based on maternal mtDNA (full sequences from 2,691 individuals, 10.5 ± 3.5 individuals per village), paternal Y chromosome (genotyping of 1,554 male individuals, 6.0 ± 2.8 individuals per village), and genome-wide SNP data (700 individuals genotyped for 2.5 M SNPs, 2.8 ± 0.70 individuals per village).  Fig. 1. Geographic distribution of Asian and African genetic ancestry across Madagascar. (A) Sampling grid across Madagascar: Three to four villages were sampled in each of 82 spots that are each 50 km in diameter. Image courtesy of Google Earth ©2016 TerraMetrics. (B) Exponential kriging interpolation of the ancestry across the Madagascar landscape based on the frequency of mtDNA lineages and Y chromosome lineages in each village and the average of Admixture (k = 3) analysis for genome-wide data based on the high-density panel. Origin of Malagasy Genomic Diversity. Phylogenetic analysis of mitochondrial lineages shows that, with the exception of M23, all other lineages have been reported outside of Madagascar and have origins in either East Asia or Africa (Fig. 2A and Fig. S1). We find no evidence of maternal gene flow from Europe or the Middle East in our sample of 2,691 mtDNA sequences. Although the ratio of Asian/African maternal lineages varies across the island, the overall frequency of East Asian and African mtDNA lineages are roughly equal. All African lineages with a frequency >1% (Fig. 2A) are associated with Bantu-speaking groups (20–22), with the exception of haplogroup L2a1b1a, which is classified by previous studies as an East African haplogroup (but still could have been brought to Madagascar by Bantu-speaking groups). Although M23 has been found only in Madagascar so far, suggesting that it arose there, M23 has a recent origin (1,200 ± 300 y BP) (Fig. S1). Hence, M23 diversity does not support an ancient settlement of Madagascar by a putative ancient pre-Bantu/pre-Austronesian population such as the hypothesized Vazimba (13). |
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Post by Admin on Apr 5, 2024 20:19:07 GMT
 Fig. 2. Uniparental lineages. (A) Distribution of mtDNA lineages according to continental origin. Asian lineages are in blue, African lineages are in red, and M23 (unknown origin) is in purple. (B) Distribution of Y chromosome lineages according to continental origin. Asian lineages are in blue, African lineages are in red, and Eurasian lineages are in green. Overall, Y chromosome lineages of African origin are much more frequent in Madagascar than are lineages of East Asian origin (70.7 vs. 20.7%), in contrast to the mtDNA lineages (42.4 African origin vs. 50.1% East Asian origin) (Fig. 2B and Fig. S1). Other Y chromosome lineages with uncertain origins are also present; some of these (R1a, J2, T1, G2) are also present in the Middle East and may reflect the Muslim influence on Madagascar and the Comoros (23, 24). Haplogroup R1b, characteristic of western Europeans, is present in low frequency (0.9%), suggesting a limited paternal contribution from western Europeans. Admixture analyses (25) of the genome-wide data, based on various datasets (Dataset S1), confirm Southeast Asian and East African Bantu groups as the major contributors and exclude any major influence from other parts of the world (Fig. 3). Admixture results at k = 3 from the high-density panel produced a clear distinction between African, East Asian, and West Eurasian populations, permitting us to estimate the frequency of each ancestry component across Madagascar (Fig. S2). On average, the African component is 59.4 ± 0.4%, and the Asian component is 36.6 ± 0.4%, whereas the West-Eurasian component is only 3.9 ± 0.1%. All studied individuals present a similar pattern associating African and East Asian components, but with considerable variation (with African ancestry ranging from 26.1 to 92.6%). |
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