Verbs in subordinate clauses are in most cases distinguished from their main clause counterparts by their tone pattern, and in a few paradigms, by different endings too.

The main differences between main and subordinate clause verbs are tonal. The reason for this is that subordinate claues are syntactically noun phrases: they can function as subject, object, or adverbial. Because of this, they are case marked like any other noun phrases; and, since the verb is the final element of a subordinate clause, it carries the case marking, as usual with noun phrases. Briefly, when clauses are non subject of the main sentence they will be in the ABSOLUTIVE case; and when subject, the SUBJECT case; and that this will be marked on the verb. Each case will be described in more detail below.

1.1 Subordinate Clause Verbs showing absolutive Case.

The difference in Tone Pattern between main and subordinate clause verbs are as shown examples below:

-Main clause: Way keenaysaa
             'She is bringing it'
-Relative Clause (when nonsubject NP): Lacagta ay keenayso
                  'the money which she is bringing'
-Complement Clause: Wuxuu sheegey iney Aamina keeneyso
                    'He said that Amina is bringing it'
 
Note the differences in the ENDINGS in each clauses: where the main clause form of a verb has endings in -aa, the subordinate clause form has -o (or optionally -id in second person singular).

The TONE PATTERN in subordinate clause verbs can be summarized by the following:

1. The last syllable becomes HIGH tone if short; FALLING tone if long.
2. If the last syllable is already high, it remains so.
 
1.2 Subject Marking on Subordinate Clause Verbs

As with other noun phrases, subject marking on clauses takes place when the clause is subject of its main sentence; and is best seen as a process operating on the absolutive case form. Again, as with other noun phrases, the marking takes place on the final element of the clause, usually the clause verb. The marking effects both the endings and the tone pattern of the verb.

In their ENDINGS, subordinate clause verbs in subject case have the same forms as main clause verbs, i.e. the change -aa to -o, id, found in absolutive case forms, will not occur.

As for TONE PATTERNS, subject marking as usual LOWERS any high or falling tone on the last syllable of the noun phrase, here the verb. (The effect of this: in both endings and tone pattern, subordinate verbs showing subject case are the same as main verbs. => but not when the main clause verb is negative, since it ends with H or Falling)

-a. Inaanan arkini waa yaab. (N.B. Our consultant does not use the full 'in-ann-ann (that-NEG-I)' form, but contracts it to 'inan'.)
'That I didn't see him is surprising.'
-b. Ma'aan arkin.
'I didn't see him.'
-c. Waxaan kuu sheegay inaanan arkin.

In (a), arkini is LOW since its embedded clause is the subject of the main clause, while the main verb yaab is H in final syllable. Note, however, that  the main verb of (b) arkin is identical in its tonal shape with its absolutive subordinate counterpart in (c).

1.3. Relative Clause

Although it behaves in a similar way with other subordinate clauses, when the subject of a relative clause is also the head of the clause, it shows a difference.

a. It shows a reduced agreement paradigm (just like the case of focused subject construction)
b. It behaves as if absolutive in tonal realization
c. In present tense forms ending in -aa or -aan, there is the same reduction in the number of persons differentiated as in past tenses but the ending -aa is also reduced to -a.

If the clause verb is showing reduced agreement, as described above, the only effect on verb endings of the clause being subject marked is that forms ending in -a will lengthen to -aa.

d. Nimanka keenayaa waa askar.
'The men who are bringing it are soldiers'
e. Gabadha lacagta keentaa waa Canab.
'The girl who brings the money is Anab'

In (d), nimanka is absolutive marked, but keenayaa is subject marked (by changing keenaya to keenayaa). In (e), gabadha is absolutive marked, but kentaa is subject marked by changing keenta to keentaa.