This answer to this question:

What's the origin of referring to female superior officers as "sir"?

establishes that this expression in Star Trek purports to have originated out-of-universe in The Wrath of Khan (although the actual script contains the word "mister" which is not the same thing).

What is the chronologically earliest reference in-universe?

Do we have a reference in Enterprise? In Discovery?

Clarification: Here, "chronologically" is referring to the presumed origin of using this expression in-universe, within the timeline as perceived by the characters, not using it in the past due to time travel (unless it sticks to the locals somehow).

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    Possibly likely candidates: T'Pol, Erika Hernandez, Captain Georgiou, Michael Burham. – ThePopMachine Oct 10 '17 at 20:03
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    So regular Earth militaries don't do things this way? – Adamant Oct 10 '17 at 21:40
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    @Adamant, apparently not conclusively. See the linked question. – ThePopMachine Oct 10 '17 at 21:41
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    @Politank-Z, For the record, in "Affliction" Tucker calls Capt. Erika Hernandez "ma'am" twice. – ThePopMachine Oct 10 '17 at 22:17
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    @ThePopMachine Geogiou is addressed as Captain, Burnham and Landry as Commander. Discovery is, thus far, negative. I also remembered Valeris tacitly ordering the crewmen to assassinate Gorkon in Star Trek VI, but they answered "yes ma'am". – Politank-Z Oct 10 '17 at 22:27

EDIT: The answer which follows appears to be the earliest mention in any series/film which aired before Star Trek: Discovery, as well as being the earliest mention in the Prime (non-Mirror) universe. Refer to this answer for a possibly more correct answer, post-Discovery, however in the Mirror Universe.

I'm going to edge out JohnP's answer (episode 5x19) with episode 5x05 "Disaster", where Troi takes command of the bridge, stardate 45156.1 (year 2368) :

O'BRIEN: I recommend we initiate emergency procedure alpha two. Bypass computer control and place all systems on manual override.

TROI: Very well.

O'BRIEN: Aye, aye, sir.

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    @JohnP, no, that wouldn't count because the question is about when female superior officers began getting addressed as "sir", not some weird exception due to impersonation, possession or some other shenanigans. – ThePopMachine Oct 11 '17 at 2:32
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    I have to admit I'm really surprised we don't have an example in any of Enterprise, Discovery, TOS, or the modern film series yet! – ThePopMachine Oct 11 '17 at 2:57
  • And nothing even for the first four seasons of TNG. This just can't be the right answer! – ThePopMachine Oct 11 '17 at 3:01
  • It certainly looks like the convention is intentionally not in effect in Discovery, as there have been ample opportunities for Capt. Georgiou, Michael Burnham, or Adm. Cornwall, .... but nothing yet.... – ThePopMachine Nov 13 '17 at 5:29
  • According to Roddenberry’s TNG writer’s guide he has been “de-militarizing” the franchise from its TOS roots, so less formalities should be expected. Officers almost never use proper military (respectful) protocol and are borderline insubordinate. BUT in-universe Discovery was BEFORE TOS... so...? – Vogon Poet Sep 24 '19 at 17:05

In Star Trek: Discovery episode 1x10, "Despite Me",

in the Mirror Universe, "Capt." Burnham kills the current captain of the ISS Shenzhou in the turbolift and then emerges on the bridge. Then we have this dialog:

KEYLA DETMER: The chair is yours, Captain.

BURNHAM: Dispose of him.

UNNAMED OFFICER: With pleasure, sir.

This places the reference in 2255, and while it's unclear whether in-universe(s) this is supposed to be a

divergent trait between the universes,

it is clearly the earliest example by over a century.

Additional note:

In addition in episode 1x12 "Vaulting Ambition", the Mirror Universe Emperor Philippa Geogiou also gets the response "Yes, sir." to an order to an underling. Unfortunately, this does even less to elucidate whether this is unique to the Mirror Universe because it could be either that, or even just something unique to the Emperor.

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    I might have given you an upvote if you hadn't begged for upvotes. – Keith Thompson Jan 9 '18 at 23:36
  • @KeithThompson: It's not begging for upvotes (I don't care), it's trying to draw attention because the currently upvoted answer (my own!) is now incorrect. – ThePopMachine Jan 10 '18 at 18:40
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    Ah, I didn't notice that you had posted both answers. I suggest editing the other answer to point to this one. Or you could have updated your original answer to include the new information. – Keith Thompson Jan 10 '18 at 20:46
  • @KeithThompson: I put a note over there. – ThePopMachine Jan 10 '18 at 20:55

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