Indian Ocean crossroads: human genetic origin and population structure in the Maldives

Abstract

The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago.

Fig. 1

The Maldives geography and their location in the Indian Ocean (insert top-left). The six main sample locations are indicated by colored dots. The island names are followed by the atoll names, and the sample sizes are indicated.

Fig. 2

The distribution of mtDNA haplogroup frequencies (>1%) in the Maldives and in the West, Central, and East regional reference populations across the northern Indian Ocean. Complete haplogroup information for the Maldives sample can be found in Supporting Information.

Fig. 3

The distribution of Y-haplogroup frequencies (>1%) in the Maldives and in the West, Central, and East regional reference populations across the northern Indian Ocean. Complete haplogroup information for the Maldives sample can be found in Supporting Information Figure S3. The list of haplogroup frequencies in the studies used for the regional reference populations can be found in Supporting Information Table S5.

Fig. 4

Gene flow between the six main sampling locations measured as 1/Fst (log-transformed and standardized; see Methods for details) for Autosomal STR (4B), mtDNA HVS1 (4C), and Y-STR (4D) data. Solid lines indicate that the two connected locations are not significantly differentiated, with increasing widths indicating higher gene flow. Dashed lines indicate significant differentiation (P-value < 0.01). Sampling locations are indicated on the map of the Maldives. The atoll names have been abbreviated using the first three letters of the name, and sample sizes (females + males) are indicated in parentheses (4A).