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Many forms formed from the perfect stem (habitav-, fec-, tetig-, and others) resemble forms of esse. It looks as if a form of esse was directly attached to the perfect stem. In perfect conjunctive an -e- seems to be added and the s>r is explained by rhotacism. In pluperfect conjunctive the -ess- is replaced with -iss-. These sound changes are easy to accept, so the analogy between the two conjugations is clearly similar.

Is this similarity between esse and perfect stem forms a coincidence? How did it come about? The corresponding forms of esse are used explicitly in the passive counterparts of these forms. Were the active forms originally perhaps a combination of an active perfect participle and esse?

The active perfect indicative forms (feci, fecisti, …) do not have this similarity to esse. I will completely ignore those forms for this question; they can be explored in separate questions. This question concerns pluperfect and future perfect of indicative and perfect and pluperfect of conjunctive. Probably the perfect active infinitive should be included as well.

There was a separate question about the vowel length in feceris and similar forms. Whether the vowel lengths match perfectly between esse and perfect stem forms, the similarity is striking.

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It's probably a coincidence.

Preface: My main source for this entire answer is The Origin of the Italic Imperfect Subjunctive by J. H. Jasanoff (Vandenhoek and Ruprecht, 1991). If this is contradicted by more recent scholarship, please feel free to correct me!

All but one of the example words given are in the second person singular, because this shows off the vowel lengths more reliably (and because it's what Jasanoff does).

Imperfect Subjunctive

The imperfect subjunctive in Latin was formed from a Proto-Italic morpheme reconstructed as *-sē-. Where this morpheme comes from is unclear, since it doesn't line up with anything in PIE, but it doesn't seem to be related to sim, sīs, sit (Proto-Italic *si-ēm, *si-ēs, *si-ēd).

In most verbs, this rhotacized: *amā-sē-s > amārēs, *face-sē-s > facerēs, and so on. But in the rare athematic verbs, the s appears as itself or assimilates: *es-sē-s > essēs, *vel-sē-s > vellēs.

When I was first learning, I was taught to form the imperfect subjunctive by attaching personal endings to the infinitive. But this isn't correct either: the infinitive was formed with an ending *-si, with a short vowel. So using this rule will get the vowel lengths wrong.

Future Perfect Indicative

This tense comes from "the S-future of the perfect". In other words, the future morpheme -(i)s- attached to the perfect stem. (The "S-future" is very common for the actual future tense in Ancient Greek: present lyō → future lysō. But in Latin, it was replaced with a relative of fiō in the first and second conjugations, and the original subjunctive in the third and fourth.)

So a form like amāveris comes from amā-v-is-(i)s. The similarity to eris seems to be coincidence: vowel reduction and rhotacism turned -is-is into -eris. But I'm not sure where eris itself (as in "you will be") comes from, so I can't be sure they're unrelated.

Perfect Subjunctive

This comes from the optative of the S-future of the perfect: the optative morpheme -ī- added on to the future perfect stem. The long vowel distinguished this from the future perfect indicative at first, but as Alex B points out, the distinction vanished by Classical times. So this amāveris comes from older amāverīs, from amā-v-is-ī-s. Once again, the similarity seems coincidental.

Notably, the S-future of the present used to be used for the actual future in Old Latin (faxō "I will do" < fac-s-ō is attested), while the optative of the S-future of the present was used for the present subjunctive (faxīs "you should do" < fac-s-īs).

Pluperfect Subjunctive

This one is formed from the subjunctive morpheme *-sē- (as seen in the imperfect) combined with the S-future of the perfect (as seen in the future perfect). Amāvissēs comes from amā-v-is-sē-s, and the additional consonant prevents both vowel reduction and rhotacism.

So this one is actually half-cognate with essēs: the -sēs ending is the same. But once again I was taught wrong: the perfect infinitive comes from amā-v-is-si, with a short vowel. That -si is (probably) not related to the subjunctive -sē except by coincidence.

Pluperfect Indicative

TODO: I don't actually know where this one comes from.

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    Great answer. There was one side note that I didn't quite understand: But in Latin, a relative of fiō and the PIE subjunctive turned into a new future tense. Are we to understand that there is a fi- somewhere in amabo and/or mittam?
    – Cerberus ♦
    Commented May 15, 2018 at 18:39
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    @Cerberus My understanding is that mittēs comes from the original subjunctive, while the -bī- in amābīs comes from bhuH "become". PIE bh turned into f at the beginning of words in Latin, but b in the middle, so the stem bhuH turned into fiō, fuī, and also that -bī-. I'll edit this in.
    – Draconis ♦
    Commented May 15, 2018 at 19:10
  • The connection between the future -bi- and fi- or fu- would be worth asking separately. If someone is wondering about that, they are unlikely to take a closer look at this question. (@Cerberus)
    – Joonas Ilmavirta ♦
    Commented May 15, 2018 at 19:17
  • @JoonasIlmavirta♦: Done!
    – Cerberus ♦
    Commented May 15, 2018 at 19:30
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    Regarding erit, L&S mentions old forms escit and esit: “fut. escit for erit, XII. Tab. ap. Gell. 20, 1, 25: esit, XII. Tab. ap. Fest. s. v. nec, p. 162 Müll.: escunt for erunt", Cic. Leg. 2, 24, 60, 3, 3, 9” Not sure what to make of it, though. Rhotatic shift is obvious, but he -c- is... interesting.
    – kkm mistrusts SE
    Commented May 16, 2018 at 8:51

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