I'm not an expert but according to Wikipedia the main culprit was tuberculosis[1], which at the time didn't have an effective cure.
These deaths could have been prevented if all the students were not concentrated into these schools.
Also it appears that the indigenous population was more susceptible to TB.
It appears that TB in the indigenous population is still a problem:
"The TB rate among Aboriginal people was almost six times greater than the overall Canadian rate in 2008 and in Nunavut, it was more than 38 times the national rate (184.4 cases per 100,000 population)." [2]
The Indian Department knew that the schools served as a conduit for the spread of disease from at least 1907 onward. Dr. Bryce was still campaigning to get them to address the issue in the 1920s.
TB is also one of the diseases brought to north america by europeans, so there is less or no natural immunity which comes from thousands of years of exposure, presumably this increased risk from “foreign” diseases still exists to an extent in indigenous populations on top of the other factors which put populations at higher risk.
No, TB was present in pre-Colombian North and South America.
TB is a very ancient disease according to [1,3] and has been present in humans since the dawn of humankind according to [2].
There is evidence of the disease in human remains from the Neolithic era and Egyptian mummies from 3000 BC. Furthermore there are references to the the disease in writing from both ancient India [5] and ancient 2700 BC China, see [4].
According to [6], seals carried TB to the Americas from Africa approximately 6000 years ago; although the Wikipedia entry for TB says that it has been "unambiguously detected" in bison remains in Wyoming dated to around 17,000 years ago. [7]
It's worth pointing out that the abstract of the Nature article appears to suggest that the pre-Columbian evidence is for a different variant of TB: "Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions."
This is completely speculative, but if post-contact TB was a different strain imported from Europe, that may explain why it took such a toll on Indigenous peoples.
I wondered about this myself, but in the second sentence of the Abstract the authors say: "This notion [that TB was introduced post-contact], however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World." As you speculate, wouldn't the aboriginal inhabitants be more susceptible to TB from Europe even if it was the same disease, but separated by perhaps thousands of years genetically.
PBS claims that by the 1900 one-seventh of every person that had ever lived had died from TB[1], and according to The World Health Organization, "About one-quarter of the world's population has a TB infection, which means people have been infected by TB bacteria but are not (yet) ill ..."[2]
Significantly, The WHO goes on to say that lifetime risk of falling ill with TB if infected is between 5 and 10 percent. The poor treatment of the aboriginal peoples alone could have caused an epidemic of TB illness due to the crowding, malnutrition, and forced displacements.
My own father had TB, I wasn't allowed to visit him in the hospital as a child that year. Fortunately, he was able to obtain the relatively new antibiotic course of therapy in the early 60's that enabled him to be cured over a long period of time.
See also the Canadian Public Health web page on TB and Aboriginal people [3].
There are several different lineages of TB, one of which is global, arrived in populations at the same time as european colonists, and arose at a time long after humans had spread across the globe.
I wasn’t able to quickly find out if there are differences in expected outcomes from different lineages in different human populations.
Pressure is building right now to fund these projects and make a proper accounting of the unmarked and uncounted dead. This is just one of dozens of crime scenes. Consider telling your MP you support this effort.
Physical harm? Malnourishment?