Comparison of material depends to some extent on the purposes of the comparison. For mere identification, a suitable key, with attention given only to the characters in it, may be enough in well-known groups. If the form is likely to be a new one, its general position is determined by observing as many characters as possible and by comparing them with the definitions and descriptions in a natural classification. The new specimen is compared with its nearest known relatives, usually with reference to type material. Any character may be of taxonomic use. In general, taxonomists tend to work from preserved material, so that their findings can be checked. For extinct forms, of course, only preserved material (fossils) is available.

Many biochemical, physiological, or behavioral characters may be at least as good as anatomical characters for discriminating between closely related species or for suggesting relationships. There has been a tendency to discount anatomical characters, but, when they are obtainable in quantity (as for most plants and animals), they probably represent as large a sample of the effects of the organism’s heredity as can be got, short of complete genetic analysis. Enthusiasts in genetics often stress that the only real basis for classification is the actual genotype of each organism—i.e., the hereditary information by which the organism is formed. It is impossible to obtain such information for extinct forms, and the time required to obtain it for most existing ones would be enormous, even if the techniques were available. An important development, however, has been the hybridization technique employing deoxyribonucleic acid (DNA), the substance by which hereditary information is coded. With this technique, it has been possible to determine similarities in parts of DNA molecules from different organisms but not the nature of their differences.

In making comparisons, resemblances resulting from convergence must be considered. Whales and bony fishes, for example, have similar body shapes for the same function—progression through water. Their internal features, however, are widely different. In this case, the convergence is evident because of the large number of characters that link whales to other mammals and not to the fishes and because the fossil record for the vertebrates provides a fair indication of the actual evolutionary sequence from primitive fishes through primitive amphibians to primitive reptiles, mammal-like reptiles, and mammals. In the absence of a good fossil record, it may be difficult or impossible to positively identify a case of convergence, yet it has been asserted that the occurrence of convergence must not be stated unless it has been “proved.” To obey this assertion would be to make the method of analysis dictate in part the results achieved.

In some forms, especially internal parasites, great modification has occurred in adapting to a parasitic way of life. The “root system” of the “tumour” (in reality a parasite) found under the abdomen (“tail”) of some crabs, for example, penetrates through the crab’s body. The parasite is unrecognizable as a close relative of the barnacles (crustaceans not far removed from the crabs themselves) without the free-swimming larval stage, which shows its affinities. Transient or inconspicuous characters may be of great importance in indicating affinities; the complete life cycle of a specimen may have to be observed before its affinities can be determined. Although such characters may be useless for identification and for definition of a natural group if only a few forms in a group show them, they may be of the utmost importance in understanding relationships. Characters are therefore weighted to some extent by the taxonomist according to their utility for different purposes. Any characters intrinsic to the organism can be used in classification. Extrinsic characters, including the position of fossils in a geological sequence and geographical distribution of fossil and recent forms, may force the taxonomist to look more closely at the intrinsic characters.

Weighting or nonweighting (i.e., by the degree of importance) of characters has been a subject of great dispute. On the one hand, it has been pointed out that weighting is often demonstrably arbitrary and always imprecise. On the other, it has been said that if characters were actually examined without weighting, some obvious cases of extreme convergence would have to be classed with each other instead of in their proper place. A classification based on unweighted characters is called a phenetic one (based on appearances) as opposed to a phyletic one (based on evolutionary change within a single line of descent), in which characters are weighted by their presumed importance in indicating lines of descent. The quarrel results in part from a misunderstanding of aims.

At present, the classification of living things is a rough, non-quantitative sketch of their diversity. A properly surveyed map of this diversity would advance classification enormously. If, on such a map, the diving petrels (Pelecanoides) of the Southern Hemisphere and the little auk (Plautus) of the Northern Hemisphere were closer to each other than to their own phylogenetic relatives (the other petrels, fulmars, and albatrosses; and the guillemots, terns, gulls, and shorebirds, respectively), this would show the extent of their convergence, which is certainly great, but it would not be a reason for combining them in a separate group. In recent years numerical techniques have been developed for estimating overall resemblance or phenetic distance. For these methods, it is necessary to use large numbers of characters taken from each form and, as far as possible, at random; this involves enormous labour. The mathematical techniques are not as yet wholly satisfactory, some having been borrowed from statistical analysis and applied to taxonomic problems without any consideration of whether they were designed to answer the questions asked by the taxonomist.

It is worth noting that if there were a complete fossil record for any group, then simply placing any form nearest to those most like it (which must be its immediate ancestors or descendants) would produce an arrangement in which all cases of parallelism and convergence would be revealed. Since evolution occurs by descent with modification, this arrangement would presumably reflect the greatest use of the information available about the group and thus would also be the most useful general arrangement. For such groups, the phenetic arrangement is the phyletic one also.