Genomic Landscape of Human Diversity Across Madagascar

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.

Citing Articles

Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance.

Shastry V, Musiani M, Novembre J bioRxiv. 2025; .

PMID: 39990319 PMC: 11844421. DOI: 10.1101/2025.02.10.637386.

Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.

Orkin J, Kuderna L, Hermosilla-Albala N, Fontsere C, Aylward M, Janiak M Nat Ecol Evol. 2024; 9(1):42-56.

PMID: 39730835 DOI: 10.1038/s41559-024-02596-1.

Montane rainforest dynamics under changes in climate and human impact during the past millennia in northern Madagascar.

Montade V, Bremond L, Teixeira H, Kasper T, Daut G, Rouland S R Soc Open Sci. 2024; 11(8):230930.

PMID: 39169961 PMC: 11335403. DOI: 10.1098/rsos.230930.

New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages.

Cabrera V Sci Rep. 2024; 14(1):11150.

PMID: 38750053 PMC: 11096394. DOI: 10.1038/s41598-024-61731-x.

Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA.

Yonezawa T, Mannen H, Honma K, Matsunaga M, Rakotondraparany F, Ratsoavina F Sci Rep. 2024; 14(1):569.

PMID: 38177203 PMC: 10766636. DOI: 10.1038/s41598-023-50708-x.

References

Maricic T, Whitten M, Paabo S . Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One. 2010; 5(11):e14004. PMC: 2982832. DOI: 10.1371/journal.pone.0014004. View

Weissensteiner H, Pacher D, Kloss-Brandstatter A, Forer L, Specht G, Bandelt H . HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016; 44(W1):W58-63. PMC: 4987869. DOI: 10.1093/nar/gkw233. View

Dewar R, Radimilahy C, Wright H, Jacobs Z, Kelly G, Berna F . Stone tools and foraging in northern Madagascar challenge Holocene extinction models. Proc Natl Acad Sci U S A. 2013; 110(31):12583-8. PMC: 3732966. DOI: 10.1073/pnas.1306100110. View

Auton A, Brooks L, Durbin R, Garrison E, Kang H, Korbel J . A global reference for human genetic variation. Nature. 2015; 526(7571):68-74. PMC: 4750478. DOI: 10.1038/nature15393. View

Tofanelli S, Bertoncini S, Castri L, Luiselli D, Calafell F, Donati G . On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol. 2009; 26(9):2109-24. DOI: 10.1093/molbev/msp120. View

Li M, Schroder R, Ni S, Madea B, Stoneking M . Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proc Natl Acad Sci U S A. 2015; 112(8):2491-6. PMC: 4345623. DOI: 10.1073/pnas.1419651112. View

Hellenthal G, Busby G, Band G, Wilson J, Capelli C, Falush D . A genetic atlas of human admixture history. Science. 2014; 343(6172):747-751. PMC: 4209567. DOI: 10.1126/science.1243518. View

Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut F, Razafindrazaka H . Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One. 2013; 8(11):e80932. PMC: 3838347. DOI: 10.1371/journal.pone.0080932. View

Kusuma P, Cox M, Pierron D, Razafindrazaka H, Brucato N, Tonasso L . Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics. 2015; 16:191. PMC: 4373124. DOI: 10.1186/s12864-015-1394-7. View

10.

Pickrell J, Pritchard J . Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8(11):e1002967. PMC: 3499260. DOI: 10.1371/journal.pgen.1002967. View

11.

Soares P, Ermini L, Thomson N, Mormina M, Rito T, Rohl A . Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet. 2009; 84(6):740-59. PMC: 2694979. DOI: 10.1016/j.ajhg.2009.05.001. View

12.

Chang C, Chow C, Tellier L, Vattikuti S, Purcell S, Lee J . Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4:7. PMC: 4342193. DOI: 10.1186/s13742-015-0047-8. View

13.

Hewitt R, Krause A, Goldman A, Campbell G, Jenkins T . Beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids. Am J Hum Genet. 1996; 58(6):1303-8. PMC: 1915062. View

14.

Browning B, Browning S . Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics. 2013; 194(2):459-71. PMC: 3664855. DOI: 10.1534/genetics.113.150029. View

15.

Rito T, Richards M, Fernandes V, Alshamali F, cerny V, Pereira L . The first modern human dispersals across Africa. PLoS One. 2013; 8(11):e80031. PMC: 3827445. DOI: 10.1371/journal.pone.0080031. View

16.

Bandelt H, Forster P, Rohl A . Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16(1):37-48. DOI: 10.1093/oxfordjournals.molbev.a026036. View

17.

Lawson D, Hellenthal G, Myers S, Falush D . Inference of population structure using dense haplotype data. PLoS Genet. 2012; 8(1):e1002453. PMC: 3266881. DOI: 10.1371/journal.pgen.1002453. View

18.

Hurles M, Sykes B, Jobling M, Forster P . The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet. 2005; 76(5):894-901. PMC: 1199379. DOI: 10.1086/430051. View

19.

Kusuma P, Brucato N, Cox M, Pierron D, Razafindrazaka H, Adelaar A . Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy. Sci Rep. 2016; 6:26066. PMC: 4870696. DOI: 10.1038/srep26066. View

20.

Pierron D, Razafindrazaka H, Pagani L, Ricaut F, Antao T, Capredon M . Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proc Natl Acad Sci U S A. 2014; 111(3):936-41. PMC: 3903192. DOI: 10.1073/pnas.1321860111. View