Newton in his first Rule of Reasoning in Philosophy states:
We are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances.
There are different ways in which one can gloss the "true" here. However, while Newton does not here explicitly clue us in no what he means by a "true cause", he immediately goes on to explain the whole principle in terms of simplicity:
To this purpose the philosophers say that Nature does nothing in vain, and more is in vain when less will serve; for Nature is pleased with simplicity, and affects not the pomp of superfluous causes.
This suggests a natural way to read "true cause," namely, it is the opposite of a superfluous cause. In other words, the first Rule suggests that we should use only those causes that we know already to be effective (with the qualification that we should do this only to the extent that these causes are sufficient for the phenomena; it is also very likely that 'cause' here should be taken in a fairly broad sense to include laws and the like). This element of Newton's first Rule we can call by its common name, the vera causa principle.
The vera causa principle, in some form or other, is a very important part of the background for the argument of Darwin's The Origin of Species. While it is not directly responsible for any of Darwin's conclusions, it plays a very important role in structuring his argument. Twice in OS he explicitly appeals to it.
1. The first instance is in the chapter on Geographical Distribution (this is a link to the first edition; if you prefer the sixth edition, here it is), when discussing "single centres of creation". Darwin looks at a debate among those who hold the opposing point of view (the theory of special creation): for each given species, was it created at a single center of creation, or were there multiple centers of creation for each species? Darwin's reply:
Undoubtedly there are many cases of extreme difficulty in understanding how the same species could possibly have migrated from some one point to the several distant and isolated points, where now found. Nevertheless the simplicity of teh view that each species was first produced within a single region captivates the mind. He who rejects it, rejects the vera causa of ordinary generation with subsequent migration, and calls in the agency of a miracle. It is universally admitted, that in most cases the area inhabited by a species is continuous; and when a plant or animal inhabits two points so distant from each other, or with an interval of such a nature, that the space could not be easily passed over by migration, the fact is given as something remarkable and exceptional.
Note the way the argument works. It is not a simple labeling of one option as a miracle and the other as a vera causa. Rather, Darwin goes on to show (in greater detail than I have quoted) that as a matter of fact, natural historians already universally explain some cases of the wide distribution of species in terms of ordinary generation with subsequent migration; it is this that makes ordinary generation with subsequent migration a vera causa. Thus, the presumption is that we should see if we can find a way for this vera causa to explain the remarkable and exceptional cases as well. Darwin provides some argument that this is possible, which I won't go into here. He will then take this vera causa of ordinary generation with subsequent migration and use it for his own purposes.
2. The second explicit appeal occurs in the conclusion:
Several eminent naturalists have of late published their belief that a multitude of reputed species in each genus are not real species; but that other species are real, that is, have been independently created. This seems to me a strange conclusion to arrive at. They admit that a multitude of forms, which till lately they themselves thought were special creations, and which are still thus looked at by the majority of naturalists, and which consequently have every external characteristic feature of true species, -- they admit that these have been produced by variation, but they refuse to extend the same view to other and very slightly different forms. Nevertheless they do not pretend that they can define, or even conjecture, which are the created forms of life, and which are those produced by secondary laws. They admit variation as a vera causa in one case, they arbitrarily reject it in another, without assigning any distinction in the two cases. The day will come when this will be given as a curious illustration of the blindness of preconceived opinion.
Here we find a similar sort of argument, which brings out an important point about vera causa reasoning: it is, in fact, a form of parity reasoning. To put it crudely, vera causa reasoning is a particular case of treating things that are the same, the same, insofar as they are the same; we can only drop the vera causa if we have, as Darwin says, something that makes it possible for us to draw a principled distinction. Implicitly, I think this argument agrees with Newton: the sort of principle of distinction one would want is that the vera causa can be shown to be simply insufficient for the phenomena. The naturalists Darwin is considering are taking variation as a vera causa -- they use it to explain certain sorts of phenomena, namely, forms that they had thought to be specially created, but which they have come to think were not. But they deny its use in other cases without giving a principled reason why the two cases are different. They are thus appearing to violate parity.
3. These, then, are the two explicit cases of Darwin's appeal to vera causa by name. It would be a mistake to think that these are the only cases of vera causa reasoning in OS, however. For instance, Darwin's starting the work with methodical and unconscious artificial selection is at least in part clearly an argument for the use of the vera causa of variation in natural cases. Another clearcut case occurs in my favorite part of the book, the discussion of the classification. Darwin is arguing that the natural system of classification, that is, the classification that characterizes the kingdoms of life as they really are in themselves, is organized genealogically. Part of his argument is that naturalists already use descent in classification:
As descent has universally been used in classing together the individuals of the same species, though the males and females and larvae are sometimes extremely different; and as it has been used in classing varieties which have undergone a certain, and sometimes a considerable amount of modification, may not this same element of descent have been unconsciously used in grouping species under genera, and genera under higher groups, though in these cases the modification has been greater in degree, and has taken a longer time to complete?
We use the element of descent in classing the individuals of both sexes and of all ages, although having few characters in common, under one species; we use descent in classing acknowledged varieties, however different they may be from their parent; and I believe this element of descent is the hidden bond of connexion which naturalists have sought under the term of the Natural System. On this idea of the natural system being, in so far as it has been perfected, genealogical in its arrangement, with the grades of difference between the descendants from a common parent, expressed by the terms genera, families, orders, &c., we can understand the rules which we are compelled to follow in our classification.
In other words, we have here a clear vera causa argument; in classification, we already use the element of descent as the principle (cause in a broad sense) for classifying individuals; we use it for classifying varieties; so Darwin suggest that we carry it over to recognizing it as the causal basis for classifying species: in other words, that we take as the principle of the natural system. And much of Darwin's discussion of the natural system involves arguing exactly what he should, given the vera causa principle: that if we do, in fact, carry it over, we find that our vera causa is sufficient for giving us a handle on the phenomena.
And this is only a selection of the most obvious cases. Thus we see that the principle of vera causa plays an important general role in OS. One of the effects it will have is that of making some of Darwin's other arguments, the arguments that relate more strictly to the theory of descent with modification, much stronger than they would be if vera causa were not also in the background. So we will see it again when we get to those arguments.