The thema can be chosen by configuring e.g.
thema: minima in
_config.yml. What theme does Github apply by default, i.e. when not explicitly setting a theme? Impossible to find out.
Also, I'd recommend using
remote_theme: jekyll/minima, so that Jekyll uses current theme code as hosted in the minima repository (or so they say).
A lot of trial-and-error goes into finding a working setup, e.g. to disable plugins (or find out which are auto-magically enabled), overriding config, etc.