Limestone deposits indicate that the location was:

once covered by water
formed by an active volcano
inhabited by mammals
affected by an earthquake

I believe the correct answer from the choices listed above is the first option. Limestone deposits indicate that the location was once covered by water. Limestone caves are often adorned with calcium carbonate formations produced through slow precipitation.

Amutation is basically the change in the gene, caused by alteration of single based units in the dna, or the genes or chromosomes were rearranged in the dna