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Environment
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According to "Canine and Feline Behavioral Therapy," female dogs may kill their puppies as a response to their environment. For example, if a dog feels that there is not an adequate supply of food, she may kill one or more of her puppies to ensure the survival of herself and the others.
Illness
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Female dogs may also kill a sickly newborn puppy as a means of preventing the spread of infection to the rest of the litter. For the mother, this has the added benefit of providing her with a meal and therefore averting a trip away from the litter. This may seem cruel to humans, but for the female dog, staying with her puppies for as long as possible is her main priority.
Contamination
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According to an article at Pet Place.com, if a female dog feels that her puppies have been contaminated or damaged in any way, she may choose to kill one or all of them. This has been to known to happen with a litter of rottweiler puppies who were killed after being taken away for tail docking.
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Why Do Female Dogs Kill Their Puppies?
To humans, seeing a female dog kill her puppies can seem an act of inexplicable cruelty. However, dog infanticide can often be explained as a response to illness, to their environment or to human intervention.