If alter self is used to assume aquatic elf form, does the form get functioning gills?

Question

The spell alter self says

You acquire the physical qualities of the new form while retaining your own mind. Physical qualities include natural size, mundane movement capabilities (such as burrowing, climbing, walking, swimming, and flight with wings, to a maximum speed of 120 feet for flying or 60 feet for nonflying movement), natural armor bonus, natural weapons (such as claws, bite, and so on), racial skill bonuses, racial bonus feats, and any gross physical qualities (presence or absence of wings, number of extremities, and so forth). A body with extra limbs does not allow you to make more attacks (or more advantageous two-weapon attacks) than normal.

You do not gain any extraordinary special attacks or special qualities not noted above under physical qualities, such as darkvision, low-light vision, blindsense, blindsight, fast healing, regeneration, scent, and so forth.

The racial traits of the aquatic elf says

Also called sea elves, these creatures are waterbreathing cousins to land-dwelling elves.…

• Gills: Aquatic elves can survive out of the water for 1 hour per point of Constitution (after that, refer to the suffocation rules).

Does a caster that uses the spell alter self to assume the form of an aquatic elf get gills that allow the caster to breathe water?

Answer 1

The traits of the aquatic elf (Monster Manual 103) are listed as extraordinary abilities in the Monster Manual (2003) and in the SRD, but they are not listed as extraordinary abilities by the premium edition Monster Manual (2012), therefore they're actually natural abilities via stealth errata. (This change is consistent throughout the premium edition and, for example, eliminates some confusion with races that had all their racial traits listed as extraordinary abilities even when those extraordinary abilities were also spell-like abilities, like some possessed by a drow (103) or a gnome (131).)

With this in mind, this DM would consider the natural ability gills of the aquatic elf a gross physical quality of the creature, therefore acquired by a creature when it assumes aquatic elf form using the 2nd-level Sor/Wiz spell alter self [trans] (Player's Handbook 197).

(It's fortunate for humanoid casters who want to breathe underwater that the aquatic elf specifically relies on the racial trait gills to breathe underwater. Many sea creatures—even humanoids like the locathah (MM 169-70)—instead rely on the subtype aquatic to breathe underwater, yet, while the subtype aquatic is specifically granted by, for example, the supernatural ability alternate form (and effects based on it like wild shape), the spell alter self doesn't add or change a creature's subtypes; getting types and subtypes takes an effect like the 4th-level Sor/Wiz spell polymorph [trans] (PH 263).)

Answer 2

While I certainly can appreciate that @HeyICanChan’s answer accounts for RAW interpretations, the OP didn’t ask for RAW and there is a much simpler answer. The spell specifically calls out “gross physical qualities”. Gills are a gross physical quality, regardless of any mechanical designations associated with it in the MM, unless you have a reason to believe that the gills (or any other analogous body part on another species) of aquatic elves who suffocate on land are somehow superfluous to their ability to exist as a living entity. Ditto waterbreathing as a result of the “aquatic” subtype. Anything more is putting undue strain on yourself and the rules.