what causes genes that are undoubtedly from an entirely different biological species to be present in a species' genome?

Answer 1

This is a fascinating question with, (I hope), an equally fascinating answer. DNA from other organisms, in this case a virus, has been spliced into the human genome for thousands of years. According to an NIH article by Vicki Contie from November 2022, "Nearly one-tenth of the human genome contains snippets of viral DNA left over from ancient infections."

While it might sound only negative for viral DNA to enter the human genome, there is a very positive application of this ability in modern-day medicine. In gene therapy, researchers create a genetic sequence that they want the recipient to have, and deliver it to the patient via Adeno-associated virus (AAV) vectors. The AAV viral vector will deliver the genetic sequence to be incorporated in the human genome. However, this time, rather than giving viral DNA that can cause illness, it is delivering a needed genetic therapy. (Also see 2019 Nature article by Wang, Tai and Gao, Adeno-associated virus vector as a platform for gene therapy delivery.