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If you end up taking a year off to have your child and spend time with him or her (which sounds like the best plan based on your posts), you can still work on manuscripts if your PI is okay with letting you work largely from home. This may erase, at least partially, any stigma of a "gap year" by showing some degree of sustained productivity,
FWIW (and not much, considering n=1), but one of my old cohortmates had a daughter (her first child) late in the summer after our first year. She took the following fall semester largely off, worked on a bit of research from home, and by November was already bored with being a stay at home mom and was ready to get back to classes, research, and clinical work. She's a great mom, too. Another classmate took a semester off to have her first child and again, was very ready to get back to school after a semester of maternity leave. Both had the support of spouses who were working full-time, YMMV, of course.
FWIW (and not much, considering n=1), but one of my old cohortmates had a daughter (her first child) late in the summer after our first year. She took the following fall semester largely off, worked on a bit of research from home, and by November was already bored with being a stay at home mom and was ready to get back to classes, research, and clinical work. She's a great mom, too. Another classmate took a semester off to have her first child and again, was very ready to get back to school after a semester of maternity leave. Both had the support of spouses who were working full-time, YMMV, of course.