ON THE NATURE OF THE AFFINITIES AND CLASSIFICATION OF ORGANIC BEINGS
 Ch. XIII of the Origin, Ed. i., Ch. XIV Ed. vi. begins with a similar statement. In the present Essay the author adds a note:--"The obviousness of the fact (i.e. the natural grouping of organisms) alone prevents it being remarkable. It is scarcely explicable by creationist: groups of aquatic, of vegetable feeders and carnivorous, &c., might resemble each other; but why as it is. So with plants,--analogical resemblance thus accounted for. Must not here enter into details." This argument is incorporated with the text in the Origin, Ed. i.
Gradual appearance and disappearance of groups.
It has been observed from the earliest times that organic beings fall into groups, and these groups into others of several values, such as species into genera, and then into sub-families, into families, orders, &c. The same fact holds with those beings which no longer exist. Groups of species seem to follow the same laws in their appearance and extinction, as do the individuals of any one species: we have reason to believe that, first, a few species appear, that their numbers increase; and that, when tending to extinction, the numbers of the species decrease, till finally the group becomes extinct, in the same way as a species becomes extinct, by the individuals becoming rarer and rarer. Moreover, groups, like the individuals of a species, appear to become extinct at different times in different countries. The Palæotherium was extinct much sooner in Europe than in India: the Trigonia was extinct in early ages in Europe, but now lives in the seas of Australia. As it happens that one species of a family will endure for a much longer period than another species, so we find that some whole groups, such as Mollusca, tend to retain their forms, or to remain persistent, for longer periods than other groups, for instance than the Mammalia. Groups therefore, in their appearance, extinction, and rate of change or succession, seem to follow nearly the same laws with the individuals of a species.
 Origin, Ed. i. p. 411, vi. p. 566.
 Origin, Ed. i. p. 316, vi. p. 457.
 Origin, Ed. i. p. 321, vi. p. 463.
 In the Origin, Ed. i. this preliminary matter is replaced (pp. 411, 412, vi. pp. 566, 567) by a discussion in which extinction is also treated, but chiefly from the point of view of the theory of divergence.
What is the Natural System?
The proper arrangement of species into groups, according to the natural system, is the object of all naturalists; but scarcely two naturalists will give the same answer to the question, What is the natural system and how are we to recognise it? The most important characters it might be thought (as it was by the earliest classifiers) ought to be drawn from those parts of the structure which determine its habits and place in the economy of nature, which we may call the final end of its existence. But nothing is further from the truth than this; how much external resemblance there is between the little otter (Chironectes) of Guiana and the common otter; or again between the common swallow and the swift; and who can doubt that the means and ends of their existence are closely similar, yet how grossly wrong would be the classification, which put close to each other a Marsupial and Placental animal, and two birds with widely different skeletons. Relations, such as in the two latter cases, or as that between the whale and fishes, are denominated "analogical," or are sometimes described as "relations of adaption." They are infinitely numerous and often very singular; but are of no use in the classification of the higher groups. How it comes, that certain parts of the structure, by which the habits and functions of the species are settled, are of no use in classification, whilst other parts, formed at the same time, are of the greatest, it would be difficult to say, on the theory of separate creations.
 Origin, Ed. i. p. 414, vi. p. 570.
 Origin, Ed. i. p. 414, vi. p. 570.
Some authors as Lamarck, Whewell &c., believe that the degree of affinity on the natural system depends on the degrees of resemblance in organs more or less physiologically important for the preservation of life. This scale of importance in the organs is admitted to be of difficult discovery. But quite independent of this, the proposition, as a general rule, must be rejected as false; though it may be partially true. For it is universally admitted that the same part or organ, which is of the highest service in classification in one group, is of very little use in another group, though in both groups, as far as we can see, the part or organ is of equal physiological importance: moreover, characters quite unimportant physiologically, such as whether the covering of the body consists of hair or feathers, whether the nostrils communicated with the mouth &c., &c., are of the highest generality in classification; even colour, which is so inconstant in many species, will sometimes well characterise even a whole group of species. Lastly, the fact, that no one character is of so much importance in determining to what great group an organism belongs, as the forms through which the embryo passes from the germ upwards to maturity, cannot be reconciled with the idea that natural classification follows according to the degrees of resemblance in the parts of most physiological importance. The affinity of the common rock-barnacle with the Crustaceans can hardly be perceived in more than a single character in its mature state, but whilst young, locomotive, and furnished with eyes, its affinity cannot be mistaken. The cause of the greater value of characters, drawn from the early stages of life, can, as we shall in a succeeding chapter see, be in a considerable degree explained, on the theory of descent, although inexplicable on the views of the creationist.
 These instances occur with others in the Origin, Ed. i. p. 416, vi. p. 572.
 Origin, Ed. i. p. 418, vi. p. 574.
 Origin, Ed. i. pp. 419, 440, vi. pp. 575, 606.
Practically, naturalists seem to classify according to the resemblance of those parts or organs which in related groups are most uniform, or vary least: thus the æstivation, or manner in which the petals etc. are folded over each other, is found to afford an unvarying character in most families of plants, and accordingly any difference in this respect would be sufficient to cause the rejection of a species from many families; but in the Rubiaceæ the æstivation is a varying character, and a botanist would not lay much stress on it, in deciding whether or not to class a new species in this family. But this rule is obviously so arbitrary a formula, that most naturalists seem to be convinced that something ulterior is represented by the natural system; they appear to think that we only discover by such similarities what the arrangement of the system is, not that such similarities make the system. We can only thus understand Linnæus' well-known saying, that the characters do not make the genus; but that the genus gives the characters: for a classification, independent of characters, is here presupposed. Hence many naturalists have said that the natural system reveals the plan of the Creator: but without it be specified whether order in time or place, or what else is meant by the plan of the Creator, such expressions appear to me to leave the question exactly where it was.
 Origin, Ed. i. pp. 418, 425, vi. pp. 574, 581.
 Origin, Ed. i. p. 413, vi. p. 569.
Some naturalists consider that the geographical position of a species may enter into the consideration of the group into which it should be placed; and most naturalists (either tacitly or openly) give value to the different groups, not solely by their relative differences in structure, but by the number of forms included in them. Thus a genus containing a few species might be, and has often been, raised into a family on the discovery of several other species. Many natural families are retained, although most closely related to other families, from including a great number of closely similar species. The more logical naturalist would perhaps, if he could, reject these two contingents in classification. From these circumstances, and especially from the undefined objects and criterions of the natural system, the number of divisions, such as genera, sub-families, families, &c., &c., has been quite arbitrary; without the clearest definition, how can it be possible to decide whether two groups of species are of equal value, and of what value? whether they should both be called genera or families; or whether one should be a genus, and the other a family?
 Origin, Ed. i. pp. 419, 427, vi. pp. 575, 582.
 This is discussed from the point of view of divergence in the Origin, Ed. i. pp. 420, 421, vi. pp. 576, 577.
 [[Footnote by the author.]] I discuss this because if Quinarism true, I false. [[The Quinary System is set forth in W. S. Macleay's Horæ Entomologicæ, 1821.]]
On the kind of relation between distinct groups.
I have only one other remark on the affinities of organic beings; that is, when two quite distinct groups approach each other, the approach is generally generic and not special; I can explain this most easily by an example: of all Rodents the Bizcacha, by certain peculiarities in its reproductive system, approaches nearest to the Marsupials; of all Marsupials the Phascolomys, on the other hand, appears to approach in the form of its teeth and intestines nearest to the Rodents; but there is no special relation between these two genera; the Bizcacha is no nearer related to the Phascolomys than to any other Marsupial in the points in which it approaches this division; nor again is the Phascolomys, in the points of structure in which it approaches the Rodents, any nearer related to the Bizcacha than to any other Rodent. Other examples might have been chosen, but I have given (from Waterhouse) this example as it illustrates another point, namely, the difficulty of determining what are analogical or adaptive and what real affinities; it seems that the teeth of the Phascolomys though appearing closely to resemble those of a Rodent are found to be built on the Marsupial type; and it is thought that these teeth and consequently the intestines may have been adapted to the peculiar life of this animal and therefore may not show any real relation. The structure in the Bizcacha that connects it with the Marsupials does not seem a peculiarity related to its manner of life, and I imagine that no one would doubt that this shows a real affinity, though not more with any one Marsupial species than with another. The difficulty of determining what relations are real and what analogical is far from surprising when no one pretends to define the meaning of the term relation or the ulterior object of all classification. We shall immediately see on the theory of descent how it comes that there should be "real" and "analogical" affinities; and why the former alone should be of value in classification--difficulties which it would be I believe impossible to explain on the ordinary theory of separate creations.
 In the corresponding passage in the Origin, Ed. i. p. 430, vi. p. 591, the term general is used in place of generic, and seems a better expression. In the margin the author gives Waterhouse as his authority.
 Origin, Ed. i. p. 430, vi. p. 591.
Classification of Races or Varieties.
Let us now for a few moments turn to the classification of the generally acknowledged varieties and subdivisions of our domestic beings; we shall find them systematically arranged in groups of higher and higher value. De Candolle has treated the varieties of the cabbage exactly as he would have done a natural family with various divisions and subdivisions. In dogs again we have one main division which may be called the family of hounds; of these, there are several (we will call them) genera, such as blood-hounds, fox-hounds, and harriers; and of each of these we have different species, as the blood-hound of Cuba and that of England; and of the latter again we have breeds truly producing their own kind, which may be called races or varieties. Here we see a classification practically used which typifies on a lesser scale that which holds good in nature. But amongst true species in the natural system and amongst domestic races the number of divisions or groups, instituted between those most alike and those most unlike, seems to be quite arbitrary. The number of the forms in both cases seems practically, whether or not it ought theoretically, to influence the denomination of groups including them. In both, geographical distribution has sometimes been used as an aid to classification; amongst varieties, I may instance, the cattle of India or the sheep of Siberia, which from possessing some characters in common permit a classification of Indian and European cattle, or Siberian and European sheep. Amongst domestic varieties we have even something very like the relations of "analogy" or "adaptation"; thus the common and Swedish turnip are both artificial varieties which strikingly resemble each other, and they fill nearly the same end in the economy of the farm-yard; but although the swede so much more resembles a turnip than its presumed parent the field cabbage, no one thinks of putting it out of the cabbages into the turnips. Thus the greyhound and racehorse, having been selected and trained for extreme fleetness for short distances, present an analogical resemblance of the same kind, but less striking as that between the little otter (Marsupial) of Guiana and the common otter; though these two otters are really less related than [[are]] the horse and dog. We are even cautioned by authors treating on varieties, to follow the natural in contradistinction of an artificial system and not, for instance, to class two varieties of the pine-apple near each other, because their fruits accidentally resemble each other closely (though the fruit may be called the final end of this plant in the economy of its world, the hothouse), but to judge from the general resemblance of the entire plants. Lastly, varieties often become extinct; sometimes from unexplained causes, sometimes from accident, but more often from the production of more useful varieties, and the less useful ones being destroyed or bred out.
 In a corresponding passage in the Origin, Ed. i. p. 423, vi. p. 579, the author makes use of his knowledge of pigeons. The pseudo-genera among dogs are discussed in Var. under Dom., Ed. ii. vol. I. p. 38.
 Origin, Ed. i. pp. 419, 427, vi. pp. 575, 582.
 Origin, Ed. i. pp. 423, 427, vi. pp. 579, 583.
 Origin, Ed. i. p. 423, vi. p. 579.
I think it cannot be doubted that the main cause of all the varieties which have descended from the aboriginal dog or dogs, or from the aboriginal wild cabbage, not being equally like or unlike--but on the contrary, obviously falling into groups and sub-groups--must in chief part be attributed to different degrees of true relationship; for instance, that the different kinds of blood-hound have descended from one stock, whilst the harriers have descended from another stock, and that both these have descended from a different stock from that which has been the parent of the several kinds of greyhound. We often hear of a florist having some choice variety and breeding from it a whole group of sub-varieties more or less characterised by the peculiarities of the parent. The case of the peach and nectarine, each with their many varieties, might have been introduced. No doubt the relationship of our different domestic breeds has been obscured in an extreme degree by their crossing; and likewise from the slight difference between many breeds it has probably often happened that a "sport" from one breed has less closely resembled its parent breed than some other breed, and has therefore been classed with the latter. Moreover the effects of a similar climate may in some cases have more than counterbalanced the similarity, consequent on a common descent, though I should think the similarity of the breeds of cattle of India or sheep of Siberia was far more probably due to the community of their descent than to the effects of climate on animals descended from different stocks.
 A general statement of the influence of conditions on variation occurs in the Origin, Ed. i. pp. 131-3, vi. pp. 164-5.
Notwithstanding these great sources of difficulty, I apprehend every one would admit, that if it were possible, a genealogical classification of our domestic varieties would be the most satisfactory one; and as far as varieties were concerned would be the natural system: in some cases it has been followed. In attempting to follow out this object a person would have to class a variety, whose parentage he did not know, by its external characters; but he would have a distinct ulterior object in view, namely, its descent in the same manner as a regular systematist seems also to have an ulterior but undefined end in all his classifications. Like the regular systematist he would not care whether his characters were drawn from more or less important organs as long as he found in the tribe which he was examining that the characters from such parts were persistent; thus amongst cattle he does value a character drawn from the form of the horns more than from the proportions of the limbs and whole body, for he finds that the shape of the horns is to a considerable degree persistent amongst cattle, whilst the bones of the limbs and body vary. No doubt as a frequent rule the more important the organ, as being less related to external influences, the less liable it is to variation; but he would expect that according to the object for which the races had been selected, parts more or less important might differ; so that characters drawn from parts generally most liable to vary, as colour, might in some instances be highly serviceable--as is the case. He would admit that general resemblances scarcely definable by language might sometimes serve to allocate a species by its nearest relation. He would be able to assign a clear reason why the close similarity of the fruit in two varieties of pine-apple, and of the so-called root in the common and Swedish turnips, and why the similar gracefulness of form in the greyhound and racehorse, are characters of little value in classification; namely, because they are the result, not of community of descent, but either of selection for a common end, or of the effects of similar external conditions.
 Origin, Ed. i. p. 423, vi. p. 579. In the margin Marshall is given as the authority.
Classification of "races" and species similar.
Thus seeing that both the classifiers of species and of varieties work by the same means, make similar distinctions in the value of the characters, and meet with similar difficulties, and that both seem to have in their classification an ulterior object in view; I cannot avoid strongly suspecting that the same cause, which has made amongst our domestic varieties groups and sub-groups, has made similar groups (but of higher values) amongst species; and that this cause is the greater or less propinquity of actual descent. The simple fact of species, both those long since extinct and those now living, being divisible into genera, families, orders &c.--divisions analogous to those into which varieties are divisible--is otherwise an inexplicable fact, and only not remarkable from its familiarity.
 Origin, Ed. i. p. 423, vi. p. 579.
Origin of genera and families.
Let us suppose for example that a species spreads and arrives at six or more different regions, or being already diffused over one wide area, let this area be divided into six distinct regions, exposed to different conditions, and with stations slightly different, not fully occupied with other species, so that six different races or species were formed by selection, each best fitted to its new habits and station. I must remark that in every case, if a species becomes modified in any one sub-region, it is probable that it will become modified in some other of the sub-regions over which it is diffused, for its organization is shown to be capable of being rendered plastic; its diffusion proves that it is able to struggle with the other inhabitants of the several sub-regions; and as the organic beings of every great region are in some degree allied, and as even the physical conditions are often in some respects alike, we might expect that a modification in structure, which gave our species some advantage over antagonist species in one sub-region, would be followed by other modifications in other of the sub-regions. The races or new species supposed to be formed would be closely related to each other; and would either form a new genus or sub-genus, or would rank (probably forming a slightly different section) in the genus to which the parent species belonged. In the course of ages, and during the contingent physical changes, it is probable that some of the six new species would be destroyed; but the same advantage, whatever it may have been (whether mere tendency to vary, or some peculiarity of organization, power of mind, or means of distribution), which in the parent-species and in its six selected and changed species-offspring, caused them to prevail over other antagonist species, would generally tend to preserve some or many of them for a long period. If then, two or three of the six species were preserved, they in their turn would, during continued changes, give rise to as many small groups of species: if the parents of these small groups were closely similar, the new species would form one great genus, barely perhaps divisible into two or three sections: but if the parents were considerably unlike, their species-offspring would, from inheriting most of the peculiarities of their parent-stocks, form either two or more sub-genera or (if the course of selection tended in different ways) genera. And lastly species descending from different species of the newly formed genera would form new genera, and such genera collectively would form a family.
 The discussion here following corresponds more or less to the Origin, Ed. i. pp. 411, 412, vi. pp. 566, 567; although the doctrine of divergence is not mentioned in this Essay (as it is in the Origin) yet the present section seems to me a distinct approximation to it.
The extermination of species follows from changes in the external conditions, and from the increase or immigration of more favoured species: and as those species which are undergoing modification in any one great region (or indeed over the world) will very often be allied ones from (as just explained) partaking of many characters, and therefore advantages in common, so the species, whose place the new or more favoured ones are seizing, from partaking of a common inferiority (whether in any particular point of structure, or of general powers of mind, of means of distribution, of capacity for variation, &c., &c.), will be apt to be allied. Consequently species of the same genus will slowly, one after the other, tend to become rarer and rarer in numbers, and finally extinct; and as each last species of several allied genera fails, even the family will become extinct. There may of course be occasional exceptions to the entire destruction of any genus or family. From what has gone before, we have seen that the slow and successive formation of several new species from the same stock will make a new genus, and the slow and successive formation of several other new species from another stock will make another genus; and if these two stocks were allied, such genera will make a new family. Now, as far as our knowledge serves, it is in this slow and gradual manner that groups of species appear on, and disappear from, the face of the earth.
The manner in which, according to our theory, the arrangement of species in groups is due to partial extinction, will perhaps be rendered clearer in the following way. Let us suppose in any one great class, for instance in the Mammalia, that every species and every variety, during each successive age, had sent down one unaltered descendant (either fossil or living) to the present time; we should then have had one enormous series, including by small gradations every known mammiferous form; and consequently the existence of groups, or chasms in the series, which in some parts are in greater width, and in some of less, is solely due to former species, and whole groups of species, not having thus sent down descendants to the present time.
 The author probably intended to write "groups separated by chasms."
With respect to the "analogical" or "adaptive" resemblances between organic beings which are not really related, I will only add, that probably the isolation of different groups of species is an important element in the production of such characters: thus we can easily see, in a large increasing island, or even a continent like Australia, stocked with only certain orders of the main classes, that the conditions would be highly favourable for species from these orders to become adapted to play parts in the economy of nature, which in other countries were performed by tribes especially adapted to such parts. We can understand how it might happen that an otter-like animal might have been formed in Australia by slow selection from the more carnivorous Marsupial types; thus we can understand that curious case in the southern hemisphere, where there are no auks (but many petrels), of a petrel having been modified into the external general form so as to play the same office in nature with the auks of the northern hemisphere; although the habits and form of the petrels and auks are normally so wholly different. It follows, from our theory, that two orders must have descended from one common stock at an immensely remote epoch; and we can perceive when a species in either order, or in both, shows some affinity to the other order, why the affinity is usually generic and not particular--that is why the Bizcacha amongst Rodents, in the points in which it is related to the Marsupial, is related to the whole group, and not particularly to the Phascolomys, which of all Marsupialia is related most to the Rodents. For the Bizcacha is related to the present Marsupialia, only from being related to their common parent-stock; and not to any one species in particular. And generally, it may be observed in the writings of most naturalists, that when an organism is described as intermediate between two great groups, its relations are not to particular species of either group, but to both groups, as wholes. A little reflection will show how exceptions (as that of the Lepidosiren, a fish closely related to particular reptiles) might occur, namely from a few descendants of those species, which at a very early period branched out from a common parent-stock and so formed the two orders or groups, having survived, in nearly their original state, to the present time.
 A similar discussion occurs in the Origin, Ed. i. p. 427, vi. p. 582.
 Puffinuria berardi, see Origin, Ed. i. p. 184, vi. p. 221.
 Origin, Ed. i. p. 430, vi. p. 591.
Finally, then, we see that all the leading facts in the affinities and classification of organic beings can be explained on the theory of the natural system being simply a genealogical one. The similarity of the principles in classifying domestic varieties and true species, both those living and extinct, is at once explained; the rules followed and difficulties met with being the same. The existence of genera, families, orders, &c., and their mutual relations, naturally ensues from extinction going on at all periods amongst the diverging descendants of a common stock. These terms of affinity, relations, families, adaptive characters, &c., which naturalists cannot avoid using, though metaphorically, cease being so, and are full of plain signification.