It is difficult to say with certainty whether the chordates’ most recent common ancestor would have lacked this gene without more information. In general, if two groups of organisms are shown to have a common ancestor, then any traits or genes that are shared by those two groups can be traced back to that common ancestor. If one of those groups is found to lack a particular gene that is present in the other group, then it is possible that the common ancestor also lacked that gene. However, this is not necessarily the case, as the gene could have been gained by one of the groups after the split from the common ancestor. Additionally, the gene could have been present in the common ancestor but lost in one of the groups. Without more information, it is impossible to say for sure whether the common ancestor would have lacked the gene in question.