Our expert says:
You are going to have to break the cycle between the JRT and your GSD female. You may to have to keep the JRT visually away from bikes and other stray dogs or even get an anti barking collar to reduce the frequency of barking. Alternatively you may have to medicate the GSD female with behavioural modifying drugs such as Clomicalm or even Prozac - short term solution and or keep her separate from the JRT.
Why don't you phone a qualified behaviourists and have a telephonic consultation (still pay a consultation) and they may discuss possible treatment solutions.
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