The earlier Malagasy sites of Lakaton’i Anja, a second millennium BCE to 14th century CE hunter–gatherer-occupied rock shelter at the northern tip of the island, and Ampasimahavelona, an 8th to 10th century CE village on the northeast coast, did not yield any ancient charred food crop remains, signaling that the earliest phase of agriculture in Madagascar may still be archaeologically invisible. Preservation of crops from all examined Madagascar sites was poor; one possibility is that early subsistence focused on vegetative crops, such as yams, taro, and banana ( 11 ), which are not represented in the types of macrobotanical records studied here but may be elucidated by future plant microfossil studies.

Length to width ratio distributions of modern and archaeological rice grains. (A) Modern japonica and indica subspecies. (B) Archaeological rice grains from Old Sima, Comoros. (C, Left) Archaeological rice grains from sites in Southeast Asia (Thailand: Noen U-Loke, Ban Non Wat, Khao Sam Kaeo, and Phu Khao Thong) and South Asia (Terr and Balathal). (C, Right) Proportion of japonica and indica markers in ancient DNA from rice grains of the same sites. (Data shown in A and C are from ref. 15 .)

This pattern contrasts sharply with the crop records found at contemporaneous sites on the Comoros Islands and Madagascar. Here, the earliest archaeobotanical assemblages date from the 8th to 10th centuries CE and are dominated by Asian crops ( Table 1 ). Rice is by far the most abundant food crop present, found at levels of approximately 70–100% in nearly all tested assemblages that produced crop remains. Rice dominated food crop assemblages from the beginning of occupation on the Comoros in the 8th century and the earliest deposits tested at the site of Mahilaka on Madagascar, a trading port established on the northwest coast in approximately the 10th century. Morphometric study of the rice grains from the 8th to 10th century site of Sima in the Comoros, the only assemblage large enough to enable this analysis, indicates the presence of both indica and japonica varieties ( Fig. S2 ). The Sima assemblage also included mung bean and cotton, both also likely from Asia (additional discussion is in Materials and Methods ). Only small quantities of African sorghum, finger millet, and cowpea were present at Sima, and African crops were absent from Mahilaka.

A clear pattern emerged in the dataset, differentiating sites dominated by African crops from sites dominated by Asian crops along a geographical cline ( Fig. 1 ). On all 11 mainland and near-coastal eastern African sites that produced identifiable crop remains, archaeobotanical assemblages contained a predominance of African crops: sorghum, pearl millet, finger millet, baobab, and/or cowpea ( Table 1 ). These crops were most likely introduced to eastern Africa from their centers of origin in western and central Africa by migrating Iron Age groups or through contact between pastoralists and hunter–gatherers with these groups ( 20 , 21 ). On these eastern African sites, Asian crops were absent or rare and mainly identified at major trading ports, such as Unguja Ukuu on Zanzibar and Tumbe on Pemba, where they were present in small quantities (approximately 8% of the total identified seeds). They occurred alongside rich evidence of Indian Ocean trade in the form of imported ceramics, glass, and metal artifacts (details in SI Text ). Significant quantities (>10%) of Asian crops do not appear at any eastern African site until the 11th century CE ( 22 ).

Our analysis revealed the presence of crops of two main origins—African and Asian—on eastern African sites. African crops consisted of millets, pulses, and fruits domesticated on the continent: sorghum (Sorghum bicolor), pearl millet (Pennisetum glaucum), finger millet (Eleusine coracana), cowpea (Vigna unguiculata), and baobab (Adansonia digitata) ( Fig. 2 ). Asian crops included Asian rice, mung bean, and cotton ( Fig. 2 ). Data on coconut was only systematically collected for the sites of Tumbe and Kimimba on Pemba, and this species is, therefore, excluded from the site comparisons presented below (these results are shown in Table S2 ). Other Asian domesticates, like banana, yam, and taro, that generally do not produce seeds were not investigated as part of this study.

Archaeobotanical Signatures of Trade and Migration.

The archaeobotanical patterns observed in mainland and near-coastal eastern Africa versus the Comoros and Madagascar show a stark contrast and suggest different histories of crop introduction to the two regions. In coastal and near-island eastern Africa, Asian crops seem to have arrived as part of commercial exchange activities, initially turning up in very small quantities and generally confined to major trading ports. There is minimal evidence for later time periods, but existing data (22, 23) suggest that Asian crops, like rice, only very gradually increased in quantity on sites in this region, reaching a peak in the 11th to 15th centuries at Chwaka on Pemba Island, where rice was, perhaps unusually, the dominant crop (22). The gradual introduction of rice to the immediate coastal eastern African region is notable and fits closely with patterns observed elsewhere for crops introduced through trade. Research across various Old World sites suggests that exotic crops introduced to a region as new plants usually featured as a minor component of subsistence systems for centuries and, in some cases, millennia after arrival before becoming a major resource (24, 25). This pattern is seen, for example, with the introduction of Asian crops at Roman Period port sites on the Red Sea (26, 27). The arrival at coastal sites in eastern Africa of rice and mung bean together with Near Eastern crops, like wheat and pea, can be understood as part of the broader acquisition of exotic goods that occurred with eastern Africa’s entry into the Indian Ocean commercial sphere (28).

In contrast, the overwhelming dominance of Asian crops in the earliest records of the Comoros and Madagascar is consistent with patterns observed when crops move through human colonization. Such a pattern is observed in Japan, where the immigration of new groups from the mainland after approximately 2,800 y B.P. is associated with the arrival of wet rice cultivation (29). It is also observed, for example, in Neolithic Europe, where the first crops are entirely Near Eastern, reflecting the arrival of migrants from this region (30). The presence of Asian crops apparently brought by migrating people on the Comoros and Madagascar is important given that Madagascar is known to have been colonized by settlers from Asia. The findings, nonetheless, require careful consideration given that there are diverse potential sources for the crops and that the present day inhabitants of the Comoros speak Bantu rather than Austronesian languages (31).

Rice and mung bean are the two main Asian food crops identified in archaeological assemblages from the Comoros and Madagascar. Fig. 3 presents a summary of Indian Ocean sites at which these two crops have been identified. Given the paucity of data for the period of 650–1200 CE, sites from an earlier period, 500 BCE to 650 CE, are also included for comparison. The fact that the combination of rice and mung bean is rare in the Near East and Arabia is notable. Indeed, it is only recorded at two Roman-period sites on the Egyptian side of the Red Sea, where it was associated with the presence of Indian traders engaged in the pepper trade (26, 27). At these sites, the crops are found in small quantities within overall assemblages dominated by Mediterranean crops. Mung bean seems to be absent from Medieval cookbooks of the Islamic world, and these sources also indicate that rice played a minor role in the cuisine of the Arab world (32). Although rice was adopted into cultivation in parts of Iran and Mesopotamia more than 2,000 y ago, it was not a staple in the Middle East in the Medieval Period (33).

Fig. 3. Distribution of archaeobotanical assemblages from the Indian Ocean region (approximately 500 BCE to 1200 CE, including sites from this study) with both mung bean and domesticated Asian rice contrasted with sites that have evidence for rice alone. Fig. S3 shows site names.

Fig. S3. Distribution of archaeobotanical assemblages from the Indian Ocean region (approximately 500 BCE to 1200 CE, including sites from this study) with both mung bean and domesticated Asian rice contrasted with sites that have evidence for rice alone. 1, Tell Guftan; 2, Tell Hrim; 3, Qaryat Medad; 4, Safat ez Zerr; 5, Tell Shheil; 6, Susa, Ville Royale; 7, Quseir al-Qadim; 8, Berenike; 9, Tumbe; 10, Unguja Ukuu; 11, Mikindani sites; 12, M'Bachile; 13, Old Sima; 14, Dembeni; 15, Mahilaka; 16, Hund; 17, Burzahom; 18, Semthan; 19, Kangra Fort; 20, Sanghol; 21, Kokhrakot; 22, Hastinapura; 23, Noh; 24, Atranjikhera; 25, Saunphari; 26, Charda; 27, Ahirua Rajarampur; 28, Sitapur; 29, Naimisharanya; 30, Sanchankot/Ramkot; 31, Radhan; 32, Hulaskera; 33, Pirvitani Sarif; 34, Kausambi; 35, Koldihwa; 36, Magha; 37, Phudzeling; 38, Mebrak; 39, Narhan; 40, Khairadih; 41, Manjhi; 42, Patliputra; 43, Rajgir; 44, Oriup (Oriyup); 45, Pakhanna (Bhairabdanga); 46, Kanmer; 47, Balathal; 48, Nagda; 49, Ujjain; 50, Dangwada; 51, Bhon; 52, Paturda; 53, Bhatkuli; 54, Kaundinyapura; 55, Khairwada; 56, Paunar; 57, Bhagimohari; 58, Adam; 59, Bhokardan; 60, Nevasa; 61, Paithan I; 62, Ter (Thair); 63, Kolhapur; 64, Piklihal IIIB/IV; 65, Veerapuram; 66, Koppa; 67, Jadigenahalli; 68, Pandawaram Dewal (Kavalgunta); 69, Fraserpet; 70, Kunnathur; 71, Guduvancheri; 72, Mallapadi; 73, Muttrapalion; 74, Arikamedu; 75, Kodumanal; 76, Perur; 77, Parambantali Hill; 78, Porunthal; 79, Mangudi; 80, Adichanallur; 81, Kantharodai; 82, Mantai; 83, Anuradhapura; 84, Tissamaharama; 85, Kirinda; 86, Wari-Bateshwar; 87, Chungliyimti; 88, New Phor; 89, Haimenkou; 90, Baodun; 91, Zhongba; 92; Mawangdui; 93, Tonglin; 94, Beiqian; 95, Shisanhang; 96, Htaukmagon; 97, Taungthaman; 98, Làng Ca; 99, Gò Chiên Vay; 100, Banyan Valley Cave; 101, Ban Ang/Phong Savanh; 102, Dong Tiên; 103, Lao Pako; 104, Nong Han Lake Kumphawapi; 105, Ban Don Ta Phet; 106, Khao Sai On; 107, Non Ban Jak; 108, Noen U-Loke; 109, Ban Non Wat; 110, Non Muang Kao; 111, Phimai sites; 112, Don Thapan; 113, Non Dua; 114, Tra Kieu; 115, Phum Snay; 116, Terrace of the Leper King; 117, Ta Phrom; 118, Angkor Wat; 119, Oc Eo/Ba Thê; 120, Thanh Diên; 121, Khao Sam Kaeo; 122, Na Sak Lot Yai; 123, Khao Sek; 124, Phu Khao Thong; 125, Satingpra; 126, Kuala Selinsing; 127, Gua Cha; 128, Yap; 129, Santiago Church; 130, Lubang Angin; 131, Pacung; 132, Sembiran.

Both rice and mung bean are, in contrast, common crops in archaeobotanical assemblages of the Indian subcontinent and Sri Lanka from at least 500 BCE onward (Fig. 3). Mung bean and indica rice are both South Asian domesticates, with domestication processes likely well underway before 1000 BCE (34, 35). Although it is, thus, possible that rice and mung bean were brought to the Comoros and Madagascar by Indian settlers, there is no other historical, linguistic, or archaeological evidence as yet to support such a colonization. The archaeobotanical absence of other South Asian crops, such as horse gram (Macrotyloma uniflorum) and urd (Vigna mungo), in the Comorian and Malagasy assemblages also suggests an introduction from outside South Asia.

Evidence of domesticated rice is common on sites in mainland Southeast Asia by the Late Prehistoric Period (approximately 300 BCE to 100 CE), reflecting the arrival of the japonica subspecies of the crop to northeast Thailand by at least 1000 BCE (15, 16, 36). Mung bean is much less prevalent archaeologically than rice in this region, although it has been recovered from some sites in southern Thailand also dating to the last two millennia (14, 37). The combination of rice and mung bean is also found at one site in Island Southeast Asia: at Pacung, in Bali, which dates to approximately the second century BCE to the second century CE (14, 34). The implications of even a minimal presence of rice and mung bean in southern Thailand and Island Southeast Asia are significant, however, given that these are the only southern Southeast Asian sites of the relevant time frame at which archaeobotanical studies have been conducted. Historical and archaeological data also suggest the likelihood of strong South Asian culinary influence on the southern Thailand-Island Southeast Asian cultural sphere because of the presence of commercial and cultural ties across the Bay of Bengal (38). Island Southeast Asia is, therefore, a feasible source for early Asian crops in the Comoros and Madagascar.

Other types of data offer additional support for this suggestion. As noted, morphometric study of the rice grains from Sima suggests the presence of both indica and japonica rice (Fig. S2). Morphometric and ancient DNA analyses of early rice assemblages from South Asia similarly show the presence of a mixed indica–japonica signal (Fig. S2) (16). Such data support the notion that most early indica cultivation was mixed, involving both indica and japonica varieties. Although archaeological rice in Island Southeast Asia has not yet been measured, a morphometric study of grains from Iron Age mainland Southeast Asian sites dating between approximately 200 BCE and 400 CE shows that assemblages there are dominated by a japonica signal (Fig. S2) (16). This pattern is in agreement with archaeobotanical models suggesting a late spread of indica rice to Southeast Asia, probably at least 1,000 y after the introduction of japonica rice (16, 36). This indica rice, which likely involved the same mix of japonica and indica seen in South Asia, probably then spread to Madagascar. Linguistic terminology, like the Dayak–Malagasy term bari/vary, a loan from Dravidian, is also suggested to trace the movement of indica rice from southern India to Borneo and then Madagascar in prehistory (39).

Morphometric analysis of rice from Chwaka on the island of Pemba has suggested the possible presence, meanwhile, of the japonica subvariety of rice (22). It is possible that rice reached eastern Africa by multiple routes at different times, with the Chwaka rice reflecting a separate rice introduction through Indian Ocean trade in the 11th to 15th centuries. Interestingly, molecular phylogenetic studies also indicate that rice as well as mung bean reached Africa as part of at least two separate dispersals, with one route in each case being linked to a potential direct Southeast Asian translocation to the Comoros or Madagascar (40, 41). Thus, despite a paucity of archaeobotanical data from the key potential source region, an Island Southeast Asian source for the early Asian crops of the Comoros and Madagascar seems to offer the best fit for the patterns observed in the available records.