what does this mean
Er, I might get some of the details wrong but...
Social anthropology is a very high victorian subject, you had physical anthropology for a while beforehand but the early 1900s is when the more "ethnographic" approach becomes quite a big thing eg Malinowski going to live with the Trobriand islanders for a while. And studying their society and how they do things.
There's two particularly famous British anthropologists, Evans Pritchards and rivers I think they are called, who studied the nuer in Africa. They are the tribe that counted cattle.
Anyway, some 70s or 80s anthropologist, can't remember his name, he basically said that all this apparent study and scholarship was never neutral, all the anthropologists all went along on colonial expedition type trips and so quite often could be said to have been sponsored by the empire machine.
And so the knowledge they produced was often tainted/used, or otherwise beneficial to the wider colonial project. So not exactly as blunt as stuff like, "oh look at these savage tribes doing terrible punishments to each other, they need civilising by us" but broadly that sort of thing and crucially allowing legitimacy for the exploitation necessary for the colonial project.
So this phrase, anthropology as the handmaiden of colonialism, comes up and sticks. The knowledge at service oc the power, sort of thing.
And I sort of, in my stoned state watching the film, thought of Aubrey and maturins relationship as exemplifying this state of affairs quite well. That sort of twin pursuit angle for well to do men on the high seas.