If you meet the requirements as outlined at http://statelaws.findlaw.com/texas-law/common-law-marriage-in-texas.html then it's no problem to file MFJ. Just understand that by doing this, if you should separate in the future it will require a legal divorce proceeding in order to change your filing status from MFJ or MFS, to Single.
For common law marriage in Texas, you have to
1. agree to be married
2. act privately as if you are married
3. tell people publicly you are married.
You are married from whenever those things happen. Filing a joint tax return for 2016 would certainly meet all three tests, since you have to agree to file jointly, and it is both a private and public declaration of your marriage. Having a formal marriage ceremony won't change that. And you would not go back and amend past returns (2015, 2014 etc) unless you believe you were married (meet all those tests) as of December 31, 2015 or December 31, 2014 etc.
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