How did Jesus get his Y chromosone?

I want to express beforehand that this is not an attack on Christianity I genuinely would like an honest answer. If Christ was a human male and Mary was his mother how did jesus get his Y chromosome. Mary is said to have given birth by immaculate conception. God in Christianity is a trinity, The Father The Son and the Holy Spirit. How did the Son happen as the Son is not the Father and is not the Holy Spirit. How can God perform a miracle in a physical world to create the Son if God didnt already belong to the physical world? If it took God 13 billion years to create chromosomes why did God suddenly choose to sidesweep all the time it took create Man and Women and cheat all the science with a miracle in Jesus's birth?