The fact, as we have seen, that all past and present organic beings can be arranged within a few great classes, in groups subordinate to groups, and with the extinct groups often falling in between the recent groups, is intelligible on the theory of natural selection with its contingencies of extinction and divergence of character. On these same principles we see how it is that the mutual affinities of the forms within each class are so complex and circuitous. We see why certain characters are far more serviceable than others for classification; why adaptive characters, though of paramount importance to the beings, are of hardly any importance in classification; why characters derived from rudimentary parts, though of no service to the beings, are often of high classificatory value; and why embryological characters are often the most valuable of all. The real affinities of all organic beings, in contradistinction to their adaptive resemblances, are due to inheritance or community of descent. The Natural System is a genealogical arrangement, with the acquired grades of difference, marked by the terms, varieties, species, genera, families, etc. ; and we have to discover the lines of descent by the most permanent characters, whatever they may be, and of however slight vital importance.

The similar framework of bones in the hand of a man, wing of a bat, fin of the porpoise, and leg of the horse⁠—the same number of vertebrae forming the neck of the giraffe and of the elephant⁠—and innumerable other such facts, at once explain themselves on the theory of descent with slow and slight successive modifications. The similarity of pattern in the wing and in the leg of a bat, though used for such different purpose⁠—in the jaws and legs of a crab⁠—in the petals, stamens, and pistils of a flower, is likewise, to a large extent, intelligible on the view of the gradual modification of parts or organs, which were aboriginally alike in an early progenitor in each of these classes. On the principle of successive variations not always supervening at an early age, and being inherited at a corresponding not early period of life, we clearly see why the embryos of mammals, birds, reptiles, and fishes should be so closely similar, and so unlike the adult forms. We may cease marvelling at the embryo of an air-breathing mammal or bird having branchial slits and arteries running in loops, like those of a fish which has to breathe the air dissolved in water by the aid of well-developed branchiae.