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The atmosphere of a planetary body (assuming it has an atmosphere) is described as being made up of distinct layers.

For example, Earth, Saturn and Jupiter all have a stratosphere and a troposphere.

What is it that defines where one layer stops and another starts?

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What is it that defines where one layer stops and another starts?

Temperature. More specifically, it's whether temperature rises or falls with increasing altitude.

In the troposphere, temperature generally decreases with increasing altitude, at an average rate of 6.4 °C/km (the environmental lapse rate). This decrease stops at the tropopause, the boundary between the troposphere and the stratosphere. The ozone layer is in the stratosphere, making temperatures in the stratosphere increase with increasing altitude. While this boundary is a bit fuzzy, it is still very real. It takes an incredibly strong thunderstorm (think hurricanes, storms powerful enough to spawn tornados, and very tall and strong storms in the Inter-Tropical Convergence Zone) to penetrate that boundary.

Temperatures in the stratosphere stop rising at the stratopause, the very fuzzy boundary between the stratosphere and the mesosphere. Like the troposphere, temperatures in the mesosphere fall (and fall very sharply) with increasing altitude. Thermodynamics makes the boundary between the stratosphere and mesosphere very different (and not nearly as clear) as the boundary between the troposphere and the mesosphere.

The boundary between the mesosphere and the thermosphere is similar to the boundary between the troposphere and stratosphere. Temperatures rise with increasing altitude in the thermosphere. This change from falling temperatures in the mesosphere to rising temperatures in the thermosphere makes for a rather stable boundary.

Something else happens near that boundary between the mesosphere and the thermosphere. Long-lived gases are fairly well-mixed in the troposphere, stratosphere, and mesosphere thanks to turbulence. Gases in the thermosphere and exosphere act more like a bunch of individual particles rather than a gas. Unlike the dense layers below, gases in the thermosphere and exosphere are differentiated. The makeup tends toward lighter and lighter particles (e.g., helium and hydrogen) with increasing altitude. Eventually, all one finds are hydrogen and helium. These are the gases that escape from the atmosphere.

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    $\begingroup$ This is a good answer, but glosses over atmospheric boundaries defined by compositional changes, for example the ionosphere. $\endgroup$ – zephyr Apr 1 '16 at 20:28
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The problematic notion here is the "distinct" layers, those effectively don't exist. Earth's atmosphere is a continuum, as any atmosphere is.

This stems from the hydrostatic pressure law $\nabla P = - g \rho$, that gives together with the ideal gas law $P = \rho k_B T / \mu$ an exponentially decaying solution with height, for pressure as well as for density. Here P is the pressure, $\rho$ is the local mass-density, g is the local gravitational acceleration, $k_B$ the Boltzmann constant and $T$ the temperature.

However there are some caveats to "layers" as a manner of characterizing the atmosphere:

  • An inversion layer can be a distinct layer where the temperature decrease with height is inversed. Thus the temperature increases for a bit, then decreases again. Therefore there will be exactly two points where the temperature increase is 0. Between those two points the definition of a distinct layer makes sense.
  • In a similar way the whole atmospheric temperature on a global scale has a funny height-dependency (see e.e. here). Again one can define layers between the points where something interesting in the T-profile happens. This is where the characterization into troposphere, stratosphere, etc. stems from.

Now we can choose variables other than temperature to characterize the atmosphere. Like ionization state, mixture state, dynamical movements, chemical makeup and then define layers that make sense only when talking about this particular variable.

Summarizing: Layers can be defined, even physically meaningful, but only in the context of a particular variable.

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The stratosphere and the troposphere are defined by the variation in temperature with height.

Within a troposphere, the temperature drops as altitude increases, and drops fast enough for convection to occur. Whereas within a stratosphere, the temperature rises with increasing altitude. Since convection requires that the rate of temperature cooling with height (the "lapse rate") exceeds the rate at which a gas cools due to a reduction in pressure, in the stratosphere the atmosphere will be stable. Tropos means "turning" and stratos means layered. The stratosphere is warmed by the absorbtion of solar radiation, particularly UV radiation (in the ozone layer), whereas the troposphere is warmed mostly from the ground, or in the case of Jupiter, from Jupiter's internal heat.

The result is that in troposphere the atmosphere will be well mixed, and clouds will form, whereas in a stratosphere there will be less mixing and far fewer clouds.

In Jupiter the tropopause (the point of lowest temperature) occurs at a pressure of about 0.1 bars. (source)

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