How did the animals that have short natural lifespans (less than a year) - and given that they were prohibited from reproduction see Rashi here - survive in the ark?
These are mainly insects such as mayflies, houseflies, dragonflies.
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The lifespan of humans of the flood generation was century-long. What makes you assume this wasn't also the case for animals?
It was only after the flood and countless disapointments from humans towards g-d that He reduced the natural lifespan of men from centuries to decades. Animals exist for the purpose of serving men. Hence I guess their lifespan also got drastically reduced
We can see from the ages given for Noach and Shem that the year of the flood did not count. For example, Noach lived 600 years before the flood and 350 years after the flood and died at the age of 950, not 951. Since the entire period of the flood was a miracle (since there should not have been room for enough food in the teivah) then it was as if aging was suspended and they resumed their lives and started aging after the flood.
And Noah was six hundred years old, and the flood came about, water upon the earth.
And Noah lived after the Flood, three hundred and fifty years.
And all the days of Noah were nine hundred and fifty years, and he died.
We see from Noach 6:21 and the medrash that Noach had to feed the animals and take care of their waste products. We also see from Rashi that none of the animals reproduced while they were in the teivah. This means that the animals that entered the teivah were the same ones that left no matter what the normal life span may have been (including those whose normal lifespan would have made them too old to reproduce after a full solar year.
and they shall swarm upon the earth: But not in the ark. This tells us that even the animals and the fowl were prohibited from mating. — [from Gen. Rabbah ad loc.]