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At first glance, higher altitudes equal lower temperatures, which would likely slow down cellular metabolism. However, while backpacking in New Mexico in ~90 degree weather, I experienced the same thing -- the flies were slow enough I was able to catch them easily in my hand, as well as with chopsticks.

Is this related to air density? Why are these flies so much slower to react and move about in the mountains.

Also, does this question even belong here?

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  • $\begingroup$ I know answers don't belong in comments but I'd say yes, this question is fine here. :) $\endgroup$ – arboviral Mar 15 '17 at 14:13
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The atmospheric density may not be the only factor, but from a physics standpoint, flying animals should in general move more slowly at high altitude.

As an example, New Mexico's Wheeler Peak is at an altitude of ~4 km above sea level. For a back-of-the-envelope air density calculation, a good estimate of scale height is 10 km, i.e. $\rho(h) = \rho_{sea}*e^{-h/10km}$ , which means the air density at Wheeler Peak is about $2/3$ the density at sea level (other air conditions being equal).
For wing-flapping animals, the power required to maintain flight is inversely proportional to the air density. I'm not confident about how flies' wing movements would be affected (this is where an entomologist should step in), but in any case their air speed should be reduced at high altitude.

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