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As you have seen, the answer is yes to both. What will happen is that certain traits or genes will be enhanced and certain traits or genes will be eliminated. Whether this is good or bad will depend on what traits you consider good. You have to be careful in selecting which chickens you select to breed so you don't encourage bad genes or traits.
Something that a lot of people seem to not consider is that if you introduce a totally new chicken, you may be introducing bad genes to your flock as well as increasing genetic diversity. Any breeding program requires that you carefully select your breeders whether inbred, linebred, or new introductions.
My mother is about to get a Japanese black tail bantam pair from a breeder. it's hard to say if the two birds are related, but I would naturally assume so. I would like a pair myself...so, if they breed and I am luck enough to get a rooster and a pullet, they would be brother and sister. If they were to breed again, in order for me to build up a good pullet to rooster ratio, then the rooster would be pairing with daughters. I was concerned that I might get one legged chicks with wings coming out thier ears....