The LimeSDR uses an internal Voltage Controlled Temperature Compensated Crystal Oscillators (VCTOXO ) which is reasonably stable, but using an external reference provides a very high level of frequency stability and accuracy.
LimeSDR uses an ADF4002 Phase Detector/Frequency Synthesizer to synchronise the 30.72 MHz VCTOXO to an external reference. There is a U.FL connector on the LimeSDR board used for the external reference, the supported frequency range is 20MHz to 300Mhz. Frequencies lower than 20MHz are supported as long as the slew rate is greater than 50 V/µs.
Leo Bodnar Electronics has a good precision GPS reference clock which works well with the LimeSDR, even at 10MHz.
The LEDs on the LimeSDR board show the status of the external reference. If LED 1 is green and blinking then the board is locked to the external reference.
Image copied from from wiki.myriadrf.org.