It is worth reiterating that while a species can be seen as a natural group, the higher levels of classification may or may not reflect biologically significant information. Such higher-level classification is an artifact of the human need to make sense of the world; it also has the practical value of organizing information, much like the way books are organized in a library. We can be sure that we are reading the same book, and studying the same organism!
Genera and other higher-level classifications are generally based on a decision to consider one or more traits as more important than others. The assignment of a particular value to a trait can seem arbitrary. Let us consider, for example, the genus Canis, which includes wolves and coyotes and the genus Vulpes, which includes foxes. The distinction between these two groups is based on smaller size and flatter skulls in Vulpes compared to Canis. Now let us examine the genus Felis, the common house cat, and the genus Panthera, which includes tigers, lions, jaguars and leopards. These two genera are distinguished by cranial features and whether (Pathera) or not (Felix) they have the ability to roar. So what do we make of these distinctions, are they really sufficient to justify distinct groups, or should Canis and Vuples (and Felix and Panthera) be merged together? Are the differences between these groups biologically meaningful? The answer is that often the basis for higher order classifications are not biologically meaningful. This common lack of biological significance is underscored by the fact that the higher order classification of an organism can change: a genus can become a family (and vice versa) or a species can be moved from one genera to another. Consider the types of organisms commonly known as bears. There are a number of different types of bear-like organisms, a fact that Linnaeus’s classification scheme acknowledged. Looking at all bear-like organisms we recognize eight types.59 We currently consider four of these, the brown bear (Ursus arctos), the Asiatic black bear (Ursus thibetanus), the American bear (Ursus americanus), and the polar bear (Ursus maritimus) to be significantly more similar to one another, based on the presence of various traits, than they are to other types of bears. We therefore placed them in their own genus, Ursus. We have placed each of the other types of bear-like organisms, the spectacled bear (Tremarctos ornatus), the sloth bear (Melurus ursinus), the sun bear (Helarctos mayalanus), and the giant panda (Ailuropoda melanoleuca) in their own separate genus, because scientists consider these species more different from one another than are the members of the genus Ursus. The problem here is how big do these differences have to be to warrant a new genus?
So where does that leave us? Here the theory of evolution together with the cell (continuity of life) theory come together. We work on the assumption that the more closely related (evolutionarily) two species are, the more traits they will share and that the development of new, biologically significant trait is what distinguishes on group from another. Traits that underlie a rational classification scheme are known as synapomorphies (a technical term); basically these are traits that appeared in one or the other branch point of a family tree and serve to define that branch point, such that organism on one branch are part of a “natural” group, distinct from those on the other branch (lineage). In just the same way that the distortion of space-time provided a reason for why there is a law of gravity, so the ancestral relationships between organisms provides a reason for why organisms can be arranged into a Linnaean hierarchy.
So the remaining question is, how do we determine ancestry when the ancestors lived, thousands, millions, or billions of years in the past. Since we cannot travel back in time, we have to deduce relationships from comparative studies of living and fossilized organisms. Here the biologist Willi Hennig played a key role.60 He established rules for using shared, empirically measurable traits to reconstruct ancestral relationships, such that each group should have a single common ancestor. As we will discover later on, one of the traits now commonly used in modern studies is gene (DNA) sequence and genomic organization data, although even here there are plenty of situations where ambiguities remain, due to the very long times that separate ancestors and present day organisms.
60 A description of Willi Hennig’s impact on taxonomy: http://www.annualreviews.org/doi/pdf....110184.000245