In Jacob 5:35 the Lord said unto his servant, "The tree profiteth me nothing, and the roots thereof profit me nothing so long as it shall bring forth evil fruit." According to Brant Gardner, this is the first time we have anything at all disparaging about the roots of the tree. Even in this case, it is not that the roots are not good (for the Lord explicitly says in the next verse, "I know that the roots are good") but simply that they "profit nothing."
The Abrahamic covenant is good, as it is the message of the gospel delivered to all of the ancient prophets. However, what is stressed here is the fact that in spiritual terms, the result of having the gospel among mankind is that it is not producing power to salvation and exaltation. The gospel might be technically "alive," however it is not producing good fruit, which is salvation and exaltation. Therefore it is producing "evil fruit."
The condition producing the evil fruit is that the wild branches "have overrun the roots" (Jacob 5:37). Remembering that the roots represent Israel's covenant relationship with the Lord, the overrunning of the roots is apparently some force that will make that covenant relationship of lesser effect such that good fruit is not produced. This may be a very apt description of the way the apostasy occurred. The mixing in of worldly ideas and philosophies (associated with the "wild branches") would become the pervasive mode of answering issues, rather than the appeal to revelation from the Lord. The weight of the intellectual world would overrun the purity of the roots representing man's ability to communicate with his Heavenly Father by covenant. The logic of the world would be subtly brought into the realm of gospel teaching. [Brant Gardner, "Brant Gardner's Page, "[http://www.highfiber.com/~nahualli/] LDStopics/Jacob/Jacob5.htm, pp. 28-31] [See the commentary on Jacob 5:11]