There are typically 2 elements, bulbs or strings of LEDS, one for the turn (brake, hazard) lights, and one for the running lights, so you will have 3 wires to each light assembly, ground, turn signal, and running lights. Since the turn signals are working this would indicate you have a good ground connection and turn signal connection. Do all of the front lights (headlights, parking lights) work? If so I would GUESS a broken wire from the back lights to the headlight switch. If none of the lights work, I would check fuses, I think the headlights are fused separately. I think I just downloaded a recent Yamaha instruction manual with the wiring, i will have to check.
Hope this helps.
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Pennsylvania, for 60+ years, most recently, Allentown, now TV. 
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