To the best of my knowledge, the U.S. government has not asserted that al Shabaab as a whole is an associated force of al Qaeda engaged in hostilities against the United States subject to the 2001 AUMF. Nonetheless, the public record reveals that we do use lethal force, from time to time, in Somalia against particular al Shabaab figures. Those strikes must depend either on an independent Article II power argument, or else on the claim that the particular target either was dual-hatted as an al Qaeda member or else had individually crossed the line (perhaps in conjunction with some larger faction within the al-Shabaab network) into "associated forces" status under the AUMF.
Against that backdrop comes news today of a drone strike on Monday targeting al Shabaab leader Mukhtar Abu Zubeyr, better known as Godane. Several years ago, Godane made a public profession of loyalty to bin Laden, and purported to place al Shabaab as a whole within the al Qaeda network (though it appears that some faction leaders within al Shabaab may not have preferred that course). Perhaps, then, the 2001 AUMF was the domestic law justification for this particular strike. Then again, bearing in mind the 120 airstrikes carried out in Iraq over the past several weeks based exclusively on Article II authorities, it is hardly obvious that the administration believes it would have to link the Godane strike to the AUMF in order to justify it in domestic law terms. Consider the possibilities:
Humanitarian grounds: The available intelligence might have suggested he was involved in plotting an attack implicating the humanitarian rationale that has been used vis-a-vis Iraq. This seems unlikely, but can't be ruled out. The possibility draws our attention, at any rate, to the question of just what sorts of threats to civilians--what scale, for example--are required to trigger this rationale.
Defense of US forces: The U.S. military has an advisory presence in Mogadishu, meant to coordinate with the Somali government effort to suppress al Shabaab. This sounds much like the U.S. military presence in Erbil and Baghdad. Might the strike on Godane, or future strikes on other al Shabaab targets, be justified on force-protection grounds akin to the arguments raised first when U.S. aircraft struck IS targets approaching Erbil and then later when the same argument was made to help explain U.S. airstrikes on IS targets at the Mosul Dam (based on the theory that collapse of the damn threatened US lives downstream in Baghdad)? Again, we can't answer without the relevant intel, but asking the question highlights the uncertain scope of the rationale.
Having a good argument that Godane was within the organizational and individual scope of the 2001 of course spares the need to contemplate such arguments, or other Article II claims that might be made (such as claims based on the need to preserve regional stability or based on the idea that Godane posed a constant (and therefore "imminent") threat to American lives apart from protecting US forces in the area). At any rate, it would be good to have a better read on just what the justification was in this instance.
UPDATE: Ryan Goodman has a good post here at Just Security elaborating the point that the administration has not (so far as we know) determined that al Shabaab as a whole has crossed into “associated forces” status.