Some kittens are born with abnormalities that humans cannot detect. For this reason they may not thrive, they may even act or smell 'wrong' to the queen. Where one or two kittens are either killed or abandoned, these kittens are often found to be somehow 'faulty'. The mother simply does not want to waste energy on raising kittens that have little chance of survival.A number of female cats will kill litters born at 'bad times of the year' in order not to use up valuable energy in raising kittens when they themselves have problems in finding adequate food.
It is well known that a mother cat may kill kittens if the nest is disturbed, especially if she is confined and cannot move or hide her litter. This is attributed to a frustrated 'protection' instinct. Unable to protect her kittens against a perceived threat, she kills them in a futile attempt at protecting them. Sometimes she will kill the kittens because they have been handled by another person or animal.
Even tom cats also kill the kittens because, Tom Cats rely greatly on scent and scent markings to determine who is present in their territory and who has visited that territory. If a tom smells the scent of a rival tomcat he may decide that the kittens belonging to his 'harem' have been fathered by the visiting tomcat. This is not in his own genetic interests. Consequently he may kill those kittens. This has two purposes. Firstly it ensures that his queens do not raise kittens fathered by a rival male. Secondly, the queens will usually come on oestrus within a few days and he can be sure of mating them so that subsequent kittens are his.
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