The above answer is correct as to the explanation of why your refund went down
Furthermore you should (almost certainly) not file as Married filing separately (MFS). Nothing you described warrants MFS. Her income will be taxed the same way MFS, and your income will be taxed at a higher rate than MFJ. But the only way to be sure is prepare returns both ways and compare.
That's more easily done with desktop software than with on line. Try this tool: <a rel="nofollow" target="_blank" href="
https://turbotax.intuit.com/tax-tools/calculators/taxcaster/?s=1">https://turbotax.intuit.com/tax-to...>
