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I have an 11 month old Anatolian Shepherd intact male, 2 year old Anatolian/Great Pyr intact female. She is in heat and well I get that the intact males will be completely stupid around her.
I have a 5 year old neutered German Shepherd and the Anatolian male has been attacking my GSD. When they are inside and the female is around (still in heat) he will overpower my GSD. When she is out of the picture and it is just the two males, the younger guy occasionally growls and barks at the older guy but other than that they get along fine and there is no problem. If all three are outside and supervised he is fine with my GSD if they are outside inside it is world War 3.
Once she is out of season will things go back to how they were and I can have all 3 inside in the same room with the young male trying not to chew the older guy's face off?
I do have the younger guy scheduled for neutering (even though it is suggested that I should wait until he is 2)
I did plan on breeding my male and female but wanted to wait and research more, but nature took its course and that is the least of my worries. I just don't want my younger male to keep attacking my older guy.
Any suggestions for how to deal with the aggression is welcome. And is this just because of hormones and him not even listening because he just wants to mate?

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Hard to say. It could be because she is in heat, and/or some temperament challenges are coming up now that the 11 month old is in adolescence. Or he is just in adolescence.

Keep them all separated when alone and supervise. This might be a wait and see thing. Tagging @JoanneF

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The other posters already commented on the "perfect storm" of things that might be happening:
  • entering adolescence leading to changes in dog-dog sociability and relationships,
  • presence of a female in heat,
  • relationships between adult neutered and intact dogs are often strained,
  • innate traits of a live stock guardian breed.

I'd just like to add something from the perspective of working with LGD breeds. I would personally treat this as a case of a young live stock guardian dog "growing into" his natural, inborn breed instincts.

LGDs (and the Anatolian Shepherd is a pretty typical example of this) were developed to be naturally suspicious of predators, including other dogs. This is why they often do best as the only pet in the household. While they can learn to live with dogs if they grew up with them, once they grow up, they tend to get along better with smaller and submissive pets. They can be pretty gentle, tolerant and protective towards them.

But also, they really do like to be "the boss". So when they live with another strong, powerful breed, especially of the same sex, things can get tricky once they enter adolescence and their dog-sociability changes. They will likely try to assert and rank themselves with other/bigger/same sex individuals, even if they grew up with them. This might be what you are seeing with your dogs. If I'm right, it's likely that things will get a bit less intense once the female is not in heat and the hormones are not quite as high, but also, some of that power play will likely continue, if left to their own devices, until they figure out their relationship.

There are different schools of thought around whether to intervene in these fights or let dogs work this out among themselves. You know your dogs best and you know if your GSD is likely to back down and defer or not - if not, this is potentially unsafe. My personal preference is to intervene and set them up for success. I don't want my dogs fighting and intimidating each other. They don't have to like each other, but they should respect and not bully each other. I have a strong preference for providing leadership and guidance, clear expectations around how I want them to behave around each other. I think knowing what to do makes them "happier" and more at ease. For this, I find a few things helpful:
1. I supervise or separate dogs that don't get along, I don't leave them alone together. I don't want them to practice unwanted behaviors.
2. I teach them to be calm around each other and respect each other's space. In your case, I would work slowly on calmness and ignoring each other, initially alone, then together in neutral places, with distance if needed and then closer, and then on their own timeline, towards being calm together indoors, in the same room etc. I would not make a big deal out of it, I would keep it light - I would just make sure they understand what the rules are.
3. I find it really helps them if they get to experience each other as working partners, preferably in an activity they were born to do. I don't know if you have access to any live stock management workshops or training, but if you do, see if you could get them to experience that and maybe eventually cooperate on these tasks. If they think of each other as partners (even better, in a team with you) rather than rivals, that usually helps.

Also, if you have not started it yet (you probably already do this, but I just thought I would mention it as a side note), start working on a "formal introductions" when a new person enters your dog's territory. Adult (especially male) LGDs tend to become naturally wary of strangers, even if they were accepting as puppies. This change sometimes takes owners by surprise, and it's not bad to have a strategy in place.
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