To see the true character of this classification, we must consider that it is based chiefly upon knowledge of existing animals.  Some extinct animals, known by their fossils, find places in it; for others new places have been made.  But it represents, on the whole, a cross-section, or cross-sections of Nature as developing in time; and, in order to give a just view of the relations of animals, it must be seen in the light of other considerations.  The older systems of classification, and the rules for making them, seem to have assumed that an actual system of classes, or of what Mill calls ‘Kinds,’ exists in nature, and that the relations of Kinds in this system are determined by quantity of resemblance in co-inherent qualities, as the ground of their affinity.

Sec. 8.  Darwin’s doctrine of the origin of species affects the conception of natural classification in several ways, (1) If all living things are blood-relations, modified in the course of ages according to their various conditions of life, ‘affinity’ must mean ’nearness of common descent’; and it seems irrational to propose a classification upon any other basis.  We have to consider the Animal (or the Vegetable) Kingdom as a family tree, exhibiting a long line of ancestors, and (descended from them) all sorts of cousins, first, second, third, etc., perhaps once, twice, or oftener ‘removed.’  Animals in the relation of first cousins must be classed as nearer than second cousins, and so on.

But, if we accept this principle, and are able to trace relationship, it may not lead to the same results as would be reached by simply relying upon the present ‘quantity of resemblance,’ unless we understand this in a very particular way.  For the most obvious features of an animal may have been recently acquired; which often happens with those characters that adapt an animal to its habits of life, as the wings of a bat, or the fish-like shape of a dolphin; or as in cases of ‘mimicry.’  Some butterflies, snakes, etc., have grown to resemble closely, in a superficial way, other butterflies and snakes, from which a stricter investigation widely separates them; and this superficial resemblance is probably a recent acquisition, for the sake of protection; the imitated butterflies being nauseous, and the imitated snakes poisonous.  On the other hand, ancient and important traits of structure may, in some species, have dwindled into inconspicuous survivals or be still found only in the embryo; so that only great knowledge and sagacity can identify them; yet upon ancient traits, though hidden, classification depends.  The seal seems nearer allied to the porpoise than to the tiger, the shrew nearer to the mouse than to the hedgehog; and the Tasmanian wolf looks more like a true wolf, the Tasmanian devil more like a badger, than like a kangaroo:  yet the seal is nearer akin to the tiger, the shrew to the hedgehog, and the Tasmanian flesh-eaters are marsupial, like the kangaroo.  To overcome this difficulty we must understand the resemblance upon which classification is based to include resemblance of Causation, that is, the fact itself of descent from common ancestors.  For organic beings, all other rules of classification are subordinate to one:  trace the genealogy of every form.