The origins of the Tutsi and Hutu peoples is a major issue in the histories of Rwanda and Burundi, as well as the Great Lakes region of Africa. While the Hutu are the ethnic majority of Rwanda, in racialist ideology originally introduced by European colonizers, the Tutsi were often identified as a separate race and also foreign, that settled amongst and intermarried with the Hutu, a Bantu group that had arrived in the region earlier, during the Bantu expansion. 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, genotype, cultural memory of inhabitants of Rwanda, and archeology/linguistics.
In comparison to the Hutu, the Tutsi have three times as much genetic influence from Nilo-Saharan populations (14.9% B) as the Hutu (4.3% B) perhaps demonstrating a Nilo-Saharan origin that supports their pastoralist historical affiliations, as opposed to the Hutu who were primarily Bantu agriculturalists.
However, a more recent study (Trombetta et al. 2015) found 22.2% E1b1b in a Tutsi sample from Burundi, but 0% in the Hutu and Twa of Burundi. Particularly of the M293 variety associated with Southern Cushitic people and East African pastoralists.