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The Datasheet provies an example configuration for when the device is powered from the bus, and shows the bus Vss connected to UGND on the avr micro, but shows a connection to earth/ground on the other GND pins. Where is this ground coming from/connected to? The usb shield connection? Tied to bus' Vss?

Example configuration

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It's the ground line on the USB cable, not the shield. The UGND and GND are connected together on the board. Here's an example of a schematic with Atmega32u4.

p.s. If you would like to learn more about connecting the USB shield on the slave device side, see this earlier question.

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