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Hynad said:
Isn't Ellie supposed to be a lesbian?

Who would be the father of her baby?

They've never explicitly said she's a lesbian, we just know she at minimum likes woman. She might only like woman, but they've probably left it slightly open on the off chance they decide a male partner would be useful to the plot (e.g. If they did want her to have a baby, but didn't want to dig into the alternative ways of that being possible).