Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean

Abstract

The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700-900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa.

Figure 1

Frequencies (%) and numbers (n) of Y haplogroups in the Comoros population sample. Haplogroup names follow the 2008 nomenclature. Branches are labelled with the binary markers tested. Numbers without a letter represent ‘M' prefixed Y markers (eg, 50=M50). Putative geographic origin is indicated for each haplogroup: Af – sub-Saharan Africa, WSA – West and Southwest Asia, SEA – Southeast Asia and ? – uncertain. Frequencies of less than 5% have been rounded up or down to the nearest unit.

Figure 2

Multidimensional scaling (MDS) analysis plot of genetic distance (Rst) calculated from the incidence of alleles at eight Y-STR loci (DYS19, 389AB, 389CD, 390, 391, 392, 393, 439). The analysis was performed with subsets of the Comoros sample, which were created on the basis of putative haplogroup origin. (a) Middle East – haplogroups E-M123, E-V22, F, G, J, L, Q and R. (b) Southeast Asian – haplogroups O, C^* and K^*. The populations represented are the Comoros (COM), this study, Madagascar (MAD), Oman (OMA),^, Turkey (TUR), North Pakistan (N-PAK), South Pakistan (S-PAK), North India (N-IND), South India (S-IND), Yemen (YEM), United Arab Emirates (UAE), Saudi Arabia (SAU), North Iran (N-IR), South Iran (S-IR),^, Malaysia (MAL), Taiwan (Paiwan) (TAI), West Borneo (East Malaysia) (W-BOR) and Bangladesh (BAN).

Figure 3

Frequencies (%) and numbers (n) of mitochondrial haplogroups in the Comoros population sample. Numbers on branches refer to the position of polymorphisms in the CRS (Cambridge reference sequence). HVS-I sequence was not determined for L0, L1, L2 or L3′4(xMN). The HVS-I SNPs are shown for M and N haplogroups, only where they provide further definition than the coding SNPs. Putative geographic origin is indicated for each haplogroup: Af – sub-Saharan Africa, SEA – Southeast Asia and ? – uncertain.

Figure 4

Multidimensional scaling (MDS) analysis plot of genetic distance (Fst) calculated from mitochondrial haplogroup frequencies. M^* and R^* were excluded from these analyses. (a) Africa, SEA and Iran – all Comoros haplogroups, except M^* and R^*. (b) and (c) MDS performed with subsets of the Comoros sample, defined on the basis of putative haplogroup origin. (b) Africa – Comoros haplogroups L. (c) SEA – Comoros and Madagascar haplogroups B4a, B4a1a1-PM, F3b, M7c1c and R9. The populations are Comoros (COM), this study, Madagascar (MAD), Central Africa (AFC), Iran (IRA), Mozambique (MOZ), Kenya (KEN), Ethopia (ETH), Tunisia (TUN), Algeria (ALG), Morocco (MOR), Mauritania (MAU), Taiwan (TAI), Philippines (PHI), Malaysia (MAL), Borneo (BOR), Sumatra (SUM), Bali (BAL) and Java (JAV).