Genesis inserts .wrap DIVs into all major HTML elements on the page. This should serve to be able to use special stylings, e.g. centering.
If you do not need the .wrap DIVs and want to reduce the DOM depth, it is recommended to remove the wrapper DIVs (.wrap).
It works like this:
add_theme_support( 'genesis-structural-wraps', array( 'header', 'menu-secondary', 'footer-widgets', 'footer' ) );
