“My theory” became “the theory” in 1869.

Again:-

“By the theory of natural selection all living species have been connected with the parent species of each genus,” &c.  We took this to mean, “By the theory of descent with modification all living species,” &c. (p. 281).

Again:-

“Some experienced conchologists are now sinking many of the very fine species of D’Orbigny and others into the rank of varieties; and on this view we do find the kind of evidence of change which on my theory we ought to find” (p. 297).

“My theory” became “the theory” in 1869.

In the fourth edition (1866), in a passage which is not in either of the two first editions, we read (p. 359), “So that here again we have undoubted evidence of change in the direction required by my theory.”  “My theory” became “the theory” in 1869; the theory of descent with modification is unquestionably intended.

Again:-

“Geological research has done scarcely anything in breaking down the distinction between species, by connecting them together by numerous, fine, intermediate varieties; and this not having been effected, is probably the gravest and most obvious of all the many objections which may be urged against my views” (p. 299).

We naturally took “my views” to mean descent with modification.  The “my” has been allowed to stand.

Again:-

“If, then, there be some degree of truth in these remarks, we have no right to expect to find in our geological formations an infinite number of those transitional forms which on my theory assuredly have connected all the past and present species of the same group in one long and branching chain of life . . .  But I do not pretend that I should ever have suspected how poor was the record in the best preserved geological sections, had not the absence of innumerable transitional links between the species which lived at the commencement and at the close of each formation pressed so hardly on my theory” (pp. 301, 302).

Substitute “descent with modification” for “my theory” and the meaning does not suffer.  The first of the two “my theories” in the passage last quoted was altered in 1869 into “our theory;” the second has been allowed to stand.

Again:-

“The abrupt manner in which whole groups of species suddenly appear in some formations, has been urged by several palaeontologists . . . as a fatal objection to the belief in the transmutation of species.  If numerous species, belonging to the same genera or families, have really started into life all at once, the fact would be fatal to the theory of descent with slow modification through natural selection” (p. 302).