New Mexicans for Science and Reason



 Updated October 31st, 2002

by Dave Thomas : (Help fight SPAM!  Please replace the AT with an @ )


This page has selected quotes from Charles Darwin and others on the subjects of hierarchy and phylogeny, concepts critical to understanding evolution.


Charles Darwin, The Origin of Species by Means of Natural Selection, 1859

Chapter 4:

"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications."

From W. F. Doolittle,. "Phylogenetic classification and the universal tree." Science 284:2124-2128, 25 June 1999 (online at ) :

Fig. 1. Part of the only figure in the Origin of Species. Darwin first uses it to represent the divergence of variants within a species, showing successively more difference in a single lineage (a1 through a10) and splitting into multiple lineages (m, s, i, and so forth), some of which will become new species. Later, he expands the tree metaphor, explaining that "limbs divided into great branches ... were themselves once, when the tree was small, budding twigs; and this connection of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups".


Chapter 13:

"Naturalists try to arrange the species, genera, and families in each class, on what is called the Natural System. But what is meant by this system? Some authors look at it merely as a scheme for arranging together those living objects which are most alike, and for separating those which are most unlike; or as an artificial means for enunciating, as briefly as possible, general propositions, that is, by one sentence to give the characters common, for instance, to all mammals, by another those common to all carnivora, by another those common to the dog-genus, and then by adding a single sentence, a full description is given of each kind of dog. The ingenuity and utility of this system are indisputable. But many naturalists think that something more is meant by the Natural System; they believe that it reveals the plan of the Creator; but unless it be specified whether order in time or space, or what else is meant by the plan of the Creator, it seems to me that nothing is thus added to our knowledge. Such expressions as that famous one of Linnaeus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent, the only known cause of the similarity of organic beings, is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications."


Charles Darwin, The Descent of Man, 1871.

From Chapter 6:

"Professor Owen, relying chiefly on the structure of the brain, has divided the mammalian series into four sub-classes. One of these he devotes to man; in another he places both the marsupials and the Monotremata; so that he makes man as distinct from all other mammals as are these two latter groups conjoined. This view has not been accepted, as far as I am aware, by any naturalist capable of forming an independent judgment, and therefore need not here be further considered.

We can understand why a classification founded on any single character or organ- even an organ so wonderfully complex and important as the brain- or on the high development of the mental faculties, is almost sure to prove unsatisfactory. This principle has indeed been tried with hymenopterous insects; but when thus long felt a profound conviction that there is a natural classed by their habits or instincts, the arrangement proved thoroughly artificial.* Classifications may, of course, be based on any character whatever, as on size, colour, or the element inhabited; but naturalists have system. This system, it is now generally admitted, must be, as far as possible, genealogical in arrangement,- that is, the co-descendants of the same form must be kept together in one group, apart from the co-descendants of any other form; but if the parent-forms are related, so will be their descendants, and the two groups together will form a larger group. The amount of difference between the several groups- that is the amount of modification which each has undergone- is expressed by such terms as genera, families, orders, and classes. As we have no record of the lines of descent, the pedigree can be discovered only by observing the degrees of resemblance between the beings which are to be classed. For this object numerous points of resemblance are of much more importance than the amount of similarity or dissimilarity in a few points. If two languages were found to resemble each other in a multitude of words and points of construction, they would be universally recognised as having sprung from a common source, notwithstanding that they differed greatly in some few words or points of construction. But with organic beings the points of resemblance must not consist of adaptations to similar habits of life: two animals may, for instance, have had their whole frames modified for living in the water, and yet they will not be brought any nearer to each other in the natural system. Hence we can see how it is that resemblances in several unimportant structures, in useless and rudimentary organs, or not now functionally active, or in an embryological condition, are by far the most serviceable for classification; for they can hardly be due to adaptations within a late period; and thus they reveal the old lines of descent or of true affinity."

* Westwood, Modern Classification of Insects, vol. ii., 1840, p. 87.


From Douglas J. Futuyma's Science on Trial, (1982, 1995) p. 53:

"One of the many reasons for believing that organisms have a common evolutionary history is that their characteristics are often hierarchically arranged. Since evolution is supposed to proceed by a series of sequential splitting events, a new characteristic that evolves in one particular branch of the tree of life is likely to be passed on to all the descendants of that branch. Within this group, another new characteristic evolves, and is then passed on to the descendants of that particular species. Thus, for example, the four-legged condition evolved in amphibians, and is retained by most of their descendants. Among these, the ancestors of the mammals evolved a single-boned lower jaw. Among some of their descendants, the rodents developed gnawing incisors, and so on. There is a nesting of groups within groups, as a consequence of common ancestry. Objects like minerals that are not descended from common ancestors cannot be arranged in this way."


Some general comments by Dave Thomas

Many classifications can be made of living species. When different features are chosen randomly, different classifications result. For example, if species were classified by, say, locomotion, we would lump birds, bees, bats and pteranodons in one class (flyers), fish, whales, and icthyosaurs in another (swimmers), humans, lizards, and ants in another (walkers), and snakes and worms in yet another (slitherers). Anyone can select a set of features and classify organisms by those features. But how do we know this pattern has any significance? Why should it be any better than another's different pattern?

Evolutionary classification is a detailed and demanding science. Comparison features should be chosen carefully. Homologous features (related by descent) are better than analogous features (related by appearance only). Shared, derived characters are preferred over ancestral features (Ridley 1986). Backbones are useless for classifying within the vertebrates; but, they are excellent for classifying vertebrates within larger groups like multi-celled animals.

When the methods of classification and phylogeny are properly applied, the concordance of the results is compelling. Lines of descent discerned from, say, comparative anatomy or paleontology, are confirmed and clarified by studies of genes and DNA. Studying evolution reveals the history of the Tree of Life itself; while there is quibbling about some of the Tree's branches, few scientists doubt its existence.


Be sure to check out Mark Ridley's Evolution and Classification: The Reformation of Cladism, Longman Group Ltd. London, 1986. This book is an excellent overview of evolutionary classifications, cladism, transformed cladism, and so forth. Ridley clearly lays out the rules for proper classification, and demolishes so-called "transformed cladism" in the process. In one discussion, Ridley notes that if we used an ancestral feature, such as number of toes, to compare an alligator, a cow, and a baboon, we would incorrectly group alligators and baboons in one group (five-toed), and cows in another (two-toed). If you can only read one book on evolution and classification, this should be the One.



David Thomas, "Example Calculation of Phylogenies: The UPGMA Method," October 2002B,


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