Nowadays, with ancient corpses, there is virtually no hope of finding chromosomial DNA in order to prove the paternity. Only chromosomial DNA could be found... to prove maternity!
About portuguese throne, illegitimate children did succeed their fathers.
In Spain it is impossible, at the same time saying Isabel II's children were not from her husband is a bit hazardous (there were disputes and reconciliations between them). Legally, they were his children.
In France too, an illegitimate child cannot succeed, however legitimate children are the queen's children. We had the example of a regent queen (Isabeau of Bavaria) who affirmed that her son (Charles VII) was not from her husband (Charles VI) but from her brother-in-law (the duke of Orléans), and there was the intervention of Saint Joan of Arc to help his son be sacred as king...
A "princess of the blood" once (in XVIIIthe century of course) told her husband : "never forget that without you, I can have princes of the blood, while without me, you can only have bastards". Not very nice but a good resume!
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