The big picture, I think, is that common ancestry is evidentially prior to natural selection in Darwin's theory and in contemporary evolutionary biology as well.

"Tiger is a natural kind" and "Tiger is a historical particular" are incompatible with each other, and evolutionary biology provides a reason for favoring the latter over the former.

The indispensability argument says (roughly) that if you have ample reason to accept an empirical scientific theory that makes indispensable use of mathematics, and that theory entails that numbers exist, then you have ample reason to accept that numbers exist. The argument affirms the antecedent of this conditional, and concludes that you have ample reason to believe that numbers exist. What is striking about this argument is that it seems to show that the empirical reasons that suffice for accepting a scientific theory also suffice for accepting a metaphysical claim.

Evolutionary theory, properly understood, does not conflict with the idea that God occasionally intervenes in nature - for example, by once or twice causing a beneficial mutation to occur. Biologists have not detected any such interventions despite the data and theory they have assembled about mutation. However, I think it is a mistake to expect biological experiments to be able to detect such one-off acts of divine intervention, especially if those acts occurred in the distant past. Science isn't in that line of work.

I think that the existence of Beethoven is remarkable, but I do not bristle at the suggestion that this event had a low probability given the initial state of the universe.

The upshot is that most philosophers of biology now hold that biological properties supervene on physical properties (where supervenience is taken to include some kind of "in virtue of" relation), and that fitness and other biological properties are not identical with physical properties.

The indispensability argument seeks to assimilate the epistemology of metaphysical statements to the epistemology of statements that are obviously empirical. I think it fails to achieve this goal. The argument does not refute the Carnapian thesis that scientific theories and metaphysical claims differ epistemologically - observations can provide evidence for the former, but not for the latter.