How did the treatment of African Americans during the last third of the 19th Century compare to that of the Indians?

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Whereas Lincoln's signing of the Emancipation Proclamation in 1863 and the Union's victory over the South in the Civil War marked a major victory for the plight of African-Americans in the United States, the last third of the 19th Century was not as kind to the native populations of North America.

African-Americans would continue to struggle for basic civil rights for another 100 years following the South's surrender in 1865.  The creation of the Ku Klux Klan and other white supremecist groups ensured that blacks would continue to be victimized, often brutally.  The fact that institutionalized segregation was only abolished with the 1954 U.S. Supreme Court decision in Brown v. the Board of Education is an apt reminder of the long, difficult path African-Americans had to traverse to achieve basic equality. 

And, yet, for all that the African-American community endured during the latter third of the 19th Century, the genocidal brutality inflicted on the Native American population represented an entirely new level of barbarity perpetrated by the United States Government.

As the westward movement of settlers of European heritage (read: Caucasian) progressed, Native American tribes were systematically eliminated or, at a minimum, forced from their ancestral lands onto far inferior "reservations" comprised of plots of land rejected for immediate development by white settlers.  Later, even many of those inferior plots of land were seized by the government with the surviving tribes forced onto even more inhospitable territory.  While African-Americans living north of the Mason-Dixon Line were able to begin to live normal lives, albeit while continuing to suffer from racial discrimination, all of the Native American tribes were subjected to inhumane treatment.