In the mitochondrial electron transport system, hydrogen atoms removed from nadh ultimately end up as part of

The answer is water. This occurs through the following reaction. During this oxidative reaction of NADH by O2, the energy expended is used to synthesize ATP from ADP and Pi.  Because NADH generated in the cytosol cannot enter the mitochondrion, electrons and protons from NADH are transferred in by an electron shuttle system.

genetic variation can be caused by mutation (which can create entirely new alleles in a population), random mating, random fertilization, and recombination between homologous chromosomes during meiosis (which reshuffles alleles within an organism's offspring).