Rebecca Wisocky nailed Gillian Anderson with an apple twice in the scene in which Mulder and Scully interview her.
A scene from Escape from the Planet of the Apes (1971) is playing on the pregnancy ward TV where the women are expecting their "special babies." It is the scene of the birth of Caesar, a super-intelligent ape regarded as a messiah.
This was originally meant to be the fifth episode but was the second to air.
In keeping with the original series run's practice of reusing Canadian character actors in multiple unrelated parts, Christine Willes, who plays Sister Mary, also appeared as FBI Agent Karen E. Kosseff (Scully's therapist) in Irresistible (1995), The Calusari (1995) and Elegy (1997).
The scientific paper that Scully mentions is most likely "Large-scale recent expansion of European patrilineages shown by population resequencing" by C. Batini, P. Hallast et al, Nature Communications, Volume 6, Article 7152 (2015). It is available for free at the U.S. National Library of Medicine Website (PubMed). In simplest terms, the title can be paraphrased: Most European men descend from a handful of Bronze Age forefathers due to a "population explosion" several thousand years ago.