According to Apple (and the substantial evidence we have at hand), throttling is done based on the performance of the battery. As the battery ages, it is less able to provide for peak current demands. This can result in the phone shutting down.
To help prevent such events, iPhone 6, 6S, 6 SE, and 7 (with higher phone versions to be included later) throttle speed when an aged, weak battery is sensed.
Swapping out the old for a new battery eliminates throttling.
Note: As of January 2, 2018, any iPhone meeting the above specs can have Apple replace the battery for $29.95. It no longer matters if the battery fails or passes the 80% capacity test. If your iPhone is more than a year old, it likely has a battery that isn't at 95-100%. 29 bucks is as inexpensive as it gets for a battery replacement.