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Both these species, Musca domestica and Drosophila melanogaster are living worldwide thanks to humans. However I have difficulties finding information about their original distribution in nature, where they come from.

University of Florida homepage states, that Musca domestica originated on the steppes of central Asia (http://entnemdept.ufl.edu/creatures/urban/flies/house_fly.htm).
For Drosophila the origin is localised to tropics of Africa and Asia.

Are these places correct? And if so, we can consider these species actually as alien species for the other parts of the world? Although, their worldwide distribution has happened long ago and nobody actually cares about their origin.

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Hi! There's a big literature on the origin of D. melanogaster.

From memory: Probably a large population-expansion around ~50 thousand years ago, followed by expansion into Europe ~10 thousand years ago (and a small population-bottle-neck at that time). Reached southwestern USA maybe as little as 50-100 years ago.

A good review is set out here: Stephan & Li Heredity (2007) 98, 65–68. doi:10.1038/sj.hdy.6800901;
"The recent demographic and adaptive history of Drosophila melanogaster"
http://www.nature.com/hdy/journal/v98/n2/full/6800901a.html

But I'm afraid it may be behind a pay-wall.