Infant mortality among feeder rodents has many causes, no matter how many you can predict, there are many more that you can't.
Therefore, since nobody responded, I guess I'll start the list and others will continue it, should they feel so inclined.
I would guess environmental conditions would be atop the list.

Things like respiratory failure, pesticide and other toxic contaminants (Even in the smallest amounts.), basically, failure to keep conditions optimal for raising their young. Basic sanitation and common sense will combat most of these.

I would guess the next most common would be conditions affecting the mother, whether they are stress related or physiological.
Lack of proper food, water, proximity to disturbances like predators, loud noises, poor climate, and having to combat other aminals to get food and water, as well as guarding her babies are all stressful. Mommies need away time too, and lack of R R takes it's toll in the way the babies are raised.
Dietary conditions would be next, I would assume. The lack of food and water is one thing, but providing lots of food that doesn't provide for the dietary requirements for the nursing mother is another. There are so many things that rat and mouse mommies require in the area of diet that I won't insult anyone and try to pass my small understanding of same as all-inclusive.
Enough fat and protein, trace elements like copper, iron, etc, vitamins, carbs to keep them all going, are all important.
Short chain fatty acids, probiotics, enzymes, and many other factors must also be provided for, as the babies will soon need to digest food on their own. These have to come from somewhere.
Mommy can't make them all, so they have to come from the native diet, as they are all locality and food source specific.

If you provide the basics and your babies are stil dying, I would guess that genetics are next, as is the size of the litter and the experience of the mother. I wouldn't be too quick to blame genetics, as most of these animals are selectively bred for large litters (High workload.) and quick turnaround.
This makes for a lot of happy babies and a skinny mommy. This (I would assume.) is the reason for their current shortened lifespan. As they get older, their fertility drops off, making them less viable as contributors and more likely to be predator fodder.

Tag, you're it.

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