[Alneyan]

You should usually not play much with reproduction, unless you have high numbers of settlers on that particular planet; population itself is only worth it when you reach fairly high numbers (a few hundred millions or one billion or two). You will get as many reproduction checks as there are populations on the planet though.

The dominant species should be determined on every turn the Atmosphere Converter is built, at least according to the newbie guide, regardless of upgrades and construction of the facility. So even if it were 100 turns after the Atmosphere Converter had been built, dropping a domining Methane population should transform that planet to a Methane atmosphere. I have never actually done so myself however, so I am just quoting the Newbie FAQ here (it makes sense given how the game works though).

Planet Shaping requires Stellar Manipulation 2 to 4, which itself requires Astrophysics 1. Stellar Manipulation has many very powerful technologies, including Warp Opening, Warp Closing, Creating and Destroying Storms, and even blowing up whole systems by destroying a star. To create a Planet, you will need asteroids and a star in the system, and a vessel equipped with a Matter Gravity Sphere.