The IRS Instructions for Married Filing Joint indicate:

A married couple filing jointly report
their combined income and deduct their
combined allowable expenses on one return. They can file a joint return even if
only one had income or if they didn't
live together all year.

https://www.irs.gov/pub/irs-pdf/i1040gi.pdf page 15. 

However on a state level you may need to review the best filing status if they have different residency status for the state.  What most people do if they run into allocation problems is create a Married Filing Joint return for Federal, and then split the return so they have a copy for Taxpayer and a copy for Spouse to complete the state returns separately.