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In what ways can we encourage musical aptitude in a two-year old?
I don't know whether you can encourage aptitude, as this is built in, but you can encourage interest. Here are some suggestions:
Naturally, a 2 year old is not going to grasp the complexity of something like music, but creating awareness, interest, and enjoyment are the first steps to something greater.
Sing to her. If you play an instrument, play to her. Play "follow the leader" with rhythms on the coffee table. Nothing you do with her will is ever wasted.
When she's older, say five, consider piano lessons. My daughters did well in a music class setting, where they met once a week with the same group of kids. The social aspect seemed to help more than private lessons, but your mileage may vary. Piano is a great place to start, because it tries in so well to reading music and music theory as they grow.