The division between highlanders and coastal dwellers has its roots in historical patterns of settlement. The original Austronesian settlers from Borneo arrived between the third and tenth centuries and established a network of principalities in the Central Highlands region conducive to growing the rice they had carried with them on their outrigger canoes. Sometime later, many settlers arrived from East Africa and established kingdoms along the relatively unpopulated coastlines. The Bantu Africans mixed with the Austronesian settlers and this resulted in the modern Malagasy people. The difference in ethnic origins remains somewhat evident between the highland and coastal regions. In addition to the ethnic distinction between highland and coastal Malagasy, one may speak of a political distinction as well. Merina monarchs in the late 18th and early 19th century, united the Merina principalities and brought the neighbouring Betsileo people under their administration first. They later extended Merina control over the majority of the coastal areas. The neighbouring island of Moheli was also ruled by a Muslim Merina dynasty founded by Abderremane, Sultan of Mohéli, who was a brother-in-law of King Radama I. The military resistance and eventual defeat of most of the coastal communities assured their subordinate position vis-à-vis the Merina-Betsileo alliance. During the 19th and 20th centuries, the French colonial administration capitalized on and further exacerbated these political inequities by appropriating existing Merina governmental infrastructure to run their colony. This legacy of political inequity dogged the people of Madagascar after gaining independence in 1960; candidates' ethnic and regional identities have often served to help or hinder their success in democratic elections. Within these two broad ethnic and political groupings, the Malagasy were historically subdivided into specifically named ethnic groups, who were primarily distinguished from one another on the basis of cultural practices. These were namely agricultural, hunting, or fishing practices; construction style of dwellings; music; hair and clothing styles; and local customs or taboos, the latter was known in the Malagasy language as fady. The number of such ethnic groups in Madagascar has been debated. The practices that distinguished many of these groups are less prevalent in the 21st century than they were in the past. But, many Malagasy are proud to proclaim their association with one or several of these groups as part of their own cultural identity.
Recent genetic studies on the Malagasy people showed that all have mixed African and Asian ancestry. Three Malagasy populations, Temoro, Vezo, and Mikea, have approx. 70% African ancestry and 30% Asian ancestry while others have lower African ancestry. In a recent island-wide survey the male-only Y chromosomes of African origin are more common than those of East Asian origin but it varies depending on the study. However the mtDNA lineages, passed down from mother to child, are the opposite. In a 2010 study, the Polynesian motif frequency varied among three ethnic groups: 50% in Merina, 22% in Vezo, and 13% in Mikea. There are two additional mutations found in all Polynesian motif carriers of Madagascar, hence named the Malagasy motif. The most likely scenario is that Madagascar was settled approximately 1,200 years ago by a very small group, which consists of approximately 30 women; where 28 of them have maritime Southeast Asian descent and 2 of them have African descent. The Malagasy population was formed from the small founding population who intermixed. The closest Asian parental population of the Malagasy are the Banjar and other South KalimantanDayak people of south east Borneo. Language footprints of their ancestors from Southeastern Asia can presently be witnessed by many shared basic vocabulary with Ma'anyan, a language from the region of the Barito River in southern Borneo.
