When creating the skeleton for rigging a character, the spine should have multiple bones for the back, then neck, head etc...

Start at the top of the penguins legs and that can be your root bone, then put in as many bones as needed up the spine, dependant on wot your requirements are for animation will help stipulate that. But you should put a joint around the shoulders areas to allow collar bone and the arm joints for the wings.

Have a look at:

https://www.simplymaya.com/movie_page...html?tut_id=36
and
https://www.simplymaya.com/movie_page...tml?tut_id=115
and
https://www.simplymaya.com/movie_page...html?tut_id=47

For rigging/weights advice also look at:

https://www.simplymaya.com/movie_page...html?tut_id=47

Good Luck