Origins of Hutu, Tutsi and Twa

The origins of the Hutu and Tutsi people is a major controversial issue in the histories of Rwanda and Burundi, as well as the Great Lakes region of Africa. The relationship between the two modern populations is thus, in many ways, derived from the perceived origins and claim to "Rwandan-ness". The largest conflicts related to this question were the Rwandan genocide, the Burundian genocide, and the First and Second Congo Wars.
Ugandan scholar Mahmoud Mamdani identifies at least four distinct foundations for studies that support the "distinct difference between Hutu and Tutsi" school of thought: phenotype and genotype, cultural memory of inhabitants of Rwanda, archeology, and linguistics.
Most Tutsis and Hutus carry the E1b1a paternal haplogroup, which is common among Bantu populations.
Genetic studies.
More recent studies have de-emphasized physical appearance, such as height and nose width, in favor of examining blood factors, the presence of the sickle cell trait, lactose intolerance in adults, and other genotype expressions. Excoffier et al. (1987) found that the Tutsi and Hima, despite being surrounded by Bantu populations, are "closer genetically to Cushites and Ethiosemites".
Another study concluded that, while the sickle cell trait among the Rwandan Hutu was comparable to that of neighboring people, it was almost non-existent among Rwandan Tutsi. Presence of the sickle cell trait is evidence of survival in the presence of malaria over many centuries, suggesting differing origins. Regional studies of the ability to digest lactose are also supportive. The ability to digest lactose among adults is widespread only among desert-dwelling nomadic groups that have depended upon milk for millennia. Three quarters of the adult Tutsi of Rwanda and Burundi have a high ability to digest lactose, while only 5% of the adults of the neighboring Shi people of eastern Congo can. Among Hutu, one in three adults has a high capacity for lactose digestion, a surprisingly high number for an agrarian people, which Mamdani suggests may be the result of centuries of intermarriage with Tutsi.
Bethwell Ogot in the 1988 UNESCO "General History" further notes that the number of pastoralists in Rwanda increased sharply around the fifteenth century. Although Luis et al. (2004) in a more general study on bi-allelic markers in many African countries found a statistically significant genetic difference between Tutsi and Hutu, the overall difference were not large.
Y-DNA (paternal).
Modern-day genetic studies of the Y-chromosome generally indicate that the Tutsi, like the Hutu, are largely of Bantu extraction (60% E1b1a, 20% B, 4% E3). Paternal genetic influences associated with the Horn of Africa and North Africa are few (under 3% E1b1b), and are ascribed to much earlier inhabitants who were assimilated. However, the Tutsi have considerably more haplogroup B paternal lineages (14.9% B) than do the Hutu (4.3% B).
Trombetta et al. (2015) found 22.2% of E1b1b in a small sample of Tutsis from Burundi, but no bearers of the haplogroup among the local Hutu and Twa populations. The subclade was of the M293 variety, which suggests that the ancestors of Tutsis in this area may have assimilated some South Cushitic pastoralists.
Autosomal DNA (overall ancestry).
In general, the Tutsi appear to share a close genetic kinship with neighboring Bantu populations, particularly the Hutu. However, it is unclear whether this similarity is primarily due to extensive genetic exchanges between these communities through intermarriage or whether it ultimately stems from common origins:
[...]generations of gene flow obliterated whatever clear-cut physical distinctions may have once existed between these two Bantu peoples – renowned to be height, body build, and facial features. With a spectrum of physical variation in the peoples, Belgian authorities legally mandated ethnic affiliation in the 1920s, based on economic criteria. Formal and discrete social divisions were consequently imposed upon ambiguous biological distinctions. To some extent, the permeability of these categories in the intervening decades helped to reify the biological distinctions, generating a taller elite and a shorter underclass, but with little relation to the gene pools that had existed a few centuries ago. The social categories are thus real, but there is little if any detectable genetic differentiation between Hutu and Tutsi.
Tishkoff et al. (2009) found their mixed Hutu and Tutsi samples from Rwanda to be predominately of Bantu origin, with minor gene flow from Afro-Asiatic communities (56.9% Afro-Asiatic genes found in the mixed Hutu/Tutsi population).
Anthropological argument.
While most supporters of the migration theory are also supporters of the "Hamitic theory", namely that the Tutsi came from the Horn of Africa, a later theory proposed that the Tutsi had instead migrated from nearby interior East Africa, and that the physical differences were the result of natural selection in a dry arid climate over millennia. Among the most detailed theories was one put forward by Jean Hiernaux, based on studies of blood factors and archeology. Noting the fossil record of a tall people with narrow facial features several thousand years ago in East Africa, including locations such as Gambles Cave in the Kenya Rift Valley and Olduvai Gorge in northern Tanzania, Hiernaux argues that while there was a migration, it was not as dramatic as some sources have proposed. He explicitly attacks the Hamitic theory that migrants from Ethiopia brought civilization to other Africans.
However, in light of recent genetic studies, Hiernaux's theory on the origin of Tutsis in East Africa appears doubtful. It has also been demonstrated that the Tutsis harbor little to no Northeastern African genetic influence on their paternal line. On the other hand, there is currently no mtDNA data available for the Tutsi, which might have helped shed light on their background.
The Rwandan myth of the Tutsi and Hutu difference was perpetuated by the Belgian Colonial Administration, helped by filmmaker Harmand Dennis during the 1930s.
Migration hypothesis vs. Hamitic hypothesis.
The colonial scholars who found complex societies in sub-Saharan Africa developed the Hamitic hypothesis. It continues to echo into the current day, both inside and outside of academic circles. As scholars developed a migration hypothesis for the origin of the Tutsi that rejected the Hamitic thesis, the notion that the Tutsi were civilizing alien conquerors was also put in question.
One school of thought noted that the influx of pastoralists around the fifteenth century may have taken place over an extended period of time and been peaceful, rather than sudden and violent. The key distinction made was that migration was not the same as conquest. Other scholars delinked the arrival of Tutsi from the development of pastoralism and the beginning of the period of statebuilding. It appears clear that pastoralism was practiced in Rwanda prior to the fifteenth century immigration, while the dates of state formation and pastoralist influx do not entirely match. This argument thus attempts to play down the importance of the pastoralist migrations.
Still other studies point out that cultural transmission can occur without actual human migration. This raises the question of how much of the changes around the fifteenth and sixteenth centuries was the result of an influx of people as opposed to the existing population being exposed to new ideas. Studies that approach the subject of racial purity are among the most controversial. These studies point out that the pastoralist migrants and pre-migration Rwandans lived side by side for centuries and practiced extensive intermarriage. The notion that current Rwandans can claim exclusively Tutsi or Hutu bloodlines is thus questioned.